So at this point we know Sean pretty well. He is quite the postmodernist. He loves to take meaningful patterns and ideas and present them to his audience (we) just to basically shove it in our face as ultimately meaningless and as a big joke. This is classic postmodernism.
So to understand NMS and Waking Titan we have to work from this basic starting point. Both are presented as cohesive universes, with the promise for some unifying meaning. But the whole point is to turn it around in our faces as a big joke.
For example, recall in NMS how SM breaks the 4th wall a few times in the lore by suggesting it is a simulation and that the creators are jaded. He is basically pointing out the fact to the NMS universe that the NMS universe is just a game and we are but players and HG is a group of jaded nerds who created it for profit. Again, this is pure postmodernism.
So some implications:
We have to realize WT is ultimately going to prove to be meaningless lore-wise. Some of it will turn out to be a joke on we the audience.
HG is Mercury is The Atlas Foundation or at least behind it. HG is the jaded organization behind the creation of Atlas. HG is the mystery hidden in plain sight. HG may even be the ones imprisoning Elizabeth Leighton. HG has always presented themselves as an antagonistic force in the NMS universe.
Don’t fall into the trap of taking this too serious. If you do, the joke is on you most of all. That is the dismal purpose of postmodernism. It loves to belittle.
So we can debate whether postmodernism has any merit (personally I despise it for a number of principled reasons), but it is the key to unlocking the literary/artistic value of NMS universe’s lore, and hence WT’s.