The first part is pretty obvious. The location fell out of range and was unloaded, so it naturally needs to be regenerated when approaching the location again.
The second part is most certainly an oversight in the game state. It’s pretty clear that the ship that is generated naturally from the seed is replaced with the living ship as a reaction to a certain game state. Only that state seems to be too narrowly defined. All in all, a very understandable and actually rather hard to catch bug. You don’t realise it until somebody actually does it.
Also, it might actually be pretty difficult to avoid. The replacement is almost certainly done by the running quest-script. At the moment you’re heading for the ship, it has all the necesesary information (i.e. it has retrieved a crashed ship location from the seed, and it knows that the living ship is supposed to be there, not anywhere else). Once you reach a location marker, that information is removed from the script, with this stage of the quest being complete (you can see this in the quest marker just vanishing once you reached it).
This happens with all missions, so is most likely part of a generic script that is reused for all of them. Once that happens, the quest doesn’t know the location anymore. There should be a very simple way to test that: Take on a mission with a specific location target (destroy a depot, raid a factory, that kind of thing). Reach the target so the marker vanishes, plant a beacon, go away and come back. My guess is that it is now not recognised as the mission location anymore, and the mission will be uncompletable.
If this holds true, changing the behavior is not actually going to be as easy as one might think. It requires the mission to hold on to the marker for longer and will require some flagging in the background, which all will affect save games. All in a script that is widely reused and generally works, which means you don’t want to change it without some serious testing afterwards. Which may well be considered to not be worth it if the occurrence of the issue is rare.