I flew into a system and found this nice looking fleet.
Something similar happened to me yesterday. Not exactly the same, but…
Try leaving the freighter, moving to another system, calling your freighter, and boarding it again.
It seems the game is getting mixed up between settings for your old freighter and your new one.
Reported and sent pics.
Funny thing. It shows a Base icon right in the doorway of the first door from the hangar.
In 3xperimental HG is trying to fix the Command Room placement, though not quite successful yet. It also appears that these invisible walls inside are new to the experimental update, or I had just not seen reports of it prior. Strange things are happening.
I have personally left my Freighter in the exact location it has been prior to Beyond, for good reason. For placing my Command Rooms I had to resort to manually adding the data in the save editor, due to a similar issue with not wanting to be placed. This was quite a while ago though.
I am assuming the new issues that came with experimental are being sorted before going live, which explains the current delay.
Funny indeed, even though it is technically a base and stored in the same location, just treated somewhat different. No reason for the icon though, which makes one wonder … 
I had no problem placing my previous command room. Now it really is unplaceable…
UPDATE
I do not know if it was today’s update or a restart but, I can now place my Command Room and access the back of my Freighter.
I’ve gotten into the habit of moving my freighter just slightly before boarding it. I have fewer problems with it if I do that first.
Glad you got it to work again. 
My freighter allowed me to put a command room down like this (by accident --not glitch building):
And of course, when deleted, it took the working one with it. :sigh:
So I am still having an issue with no power in the rear cargo area of my Freighter. I will report it again. Anyone else still having an issue?
It’s this ambient hue & in particular the sort of misted/smokeyness, (on less bright TV settings), that has had me take a break from actually playing NMS for a while.
The first is just a bit annoying but the 2nd actually strains my eyes. It was introduced with Next or Beyond & has bothered me ever since.
If I set the TV to Dynamic, it’s crystal clear but just too piercing if playing at night, yet if left on a lesser setting, the fogginess is too intrusive & the discomfort results in me shutting it off.
I’m sad to say I haven’t actually played in many weeks now…
I’m hoping the next update addresses some of these aesthetic issues…& maybe introduces a few variations in freighter layouts.
I’ve also had freighter power issues trying to place lights. It’s strangely erratic for me, not just toward the back of the base. They seem to work anywhere in the rooms right near my bridge. Elsewhere they tend to only work when placed closer to the center of the rooms. Even that’s inconsistent though.
I’m also very frustrated at not being able to place the Cross Junction anywhere on the first floor (or sometimes elsewhere) anymore.
I filed 3 separate reports today, lol. Maybe there will be some results. 
I still have a lost frigate. Lol.
Let me try explain what I think is happening.
On a freighter the main power comes from the AIRLCKCONNECTOR, which is the open doorway where you actually enter the freighter base, just up the last stairs. This provides energy storage of 1000 with a rate of 10000. This is similar to the free power connected to a base computer on a planet in creative mode when ‘free power’ is activated. However, instead of a huge range to cover the full base range (1000u), it only covers 4.1u radius, enough to just overlap with the next rooms/hallways connected.
Each room/hallway has a 4.1u radius in which it looks for a power connection and if available, passes it on using this same radius, like a bubble or sphere. Now with the ‘airlckconnector’ having all the power, the connected rooms towards the bridge, each have their own bubble of 4.1u radius. This works like a chain, where these bubbles overlap and are passing on power. The BRIDGECONNECTOR is an odd one out, as it has a bubble looking for and passing on power at a radius of 35u instead. This is why power is never an issue when building close to the bridge.
Now move further away from the bridge and you will fully rely on the bubbles from each room/hallway of 4.1u radius. Each room is 8u*8u*4u (l*w*h) with their bubble at the center of the floor. Each hallway has the same bubble radius of 4.1 and is either straight, l-shaped, or x-shaped, acting the same as a room.
Each object that is related to power use, has a bubble of its own as well. The radius of this bubble as well as origin (location relative to the object) can vary. These values can all be found in the source files however. A small coloured light for example, has a value of 0.447u for a radius to look for and pass on power. A large hydroponic tray has a value of 1.5u, a small one a value of 1u. A health station has a value of 0.63u, and a shield station a value of 0.62u. And so on for other objects.
Now when you try to visualize all these bubbles for each object placed, to see if it connects to a bubble that ‘produces’ power in the chain, you will find there are edge cases. These edge cases are actually quite easily found once you realise how it works. I will try to show an example below, where the bubbles looking for and passing on power are shown in green. The white objects are a representation of room and connected hallway:
Side view
Top-down
Now let’s add the Health Station (0.63u) and you will see how this bubble does not connect to other bubbles to receive and/or pass on power.
Another example that explains why a large hydroponic tray is not receiving power when placed right in the middle of 4 rooms.
These edge case issues appear to be consistent with the values and calculations after having done quite a bit of research on this with the release of Beyond. I have reported this in full detail to Hello Games and am hoping they will fix this with a future update. It actually (no longer) amazes me how they had not foreseen this issue to begin with.
Hope this explains it all. I could be wrong though, but I doubt it in this case.
Edit: Including the default freighter layout, where the small blue sphere is the AIRLCKCONNECTOR and the large blue sphere is the BRIDGECONNECTOR
Excellent detective work & explanation!
Interesting. In my Freighter, I have tried to create the illusion of more space than is actually there. One thing I did was replace the straight hallways leading to the cargo area with 2 curved hallways thus creating an S-shaped hallway. So I likely created another ‘no power’ bubble without knowing it. (I might add that I had some trouble placing these but eventually made it work)
I have these S-shaped hallways on both sides leading into the cargo area. I also have a 3-way hall junction in the center of my cargo area. I have used these in several places on my Freighter. One to create a small bunk area. It sits in the middle between the 2 S-shaped hallways before entering the cargo area. I have the new exocraft station between the 2 hallways, facing into the the cargo area.
I am sure this is not to scale, but I have never used Blender, 
My Appearance Modifier, Storage and Exo Comms all work fine. I tested wall lights and this is what I came up with. There is no issue with lights at the front but no power to lights in the cargo area. The problem begins in the area you mentioned.
Now both lights are working on the back of the hangar entrance area…I give up!
In some of your pictures I can see those edge cases, where in others it is not quite clear. It is certainly odd to have lights working one moment and non-functional the next. The ‘racetracks’ as you have shown before, should not be visible at all. These tracks are from freighter interior parts below, clipping through your floor. All-in-all pretty annoying to have these issues.
Do you ever move your freighter to other spots in the same system or possibly other systems? You might want to give that a try, although it will not fix the power issues, it has fixed weird clipping issues for others.
Either way, I really hope HG plans on fixing this. There should be no need for power issues on the freighter to begin with. For all I care they could have just added a power source that covers the full possible area you are allowed to build in. That would fix it once and for all, but instead they used a different approach, prone to failure.
