Well, after thinking about how much effort would have to go into finding creative and interesting ways to seemlessly merge 3 distinct looks (alien, Dwemer and organic) into a single graduated style of architecture, I'm not so sure about it either, lol. It would be a nice touch, I think, and depending on what you plan to do it could give some clues to the backstory, but I have to wonder how well we'd be able to pull it off. Too bad we're not trained, professional game developers.
I especially like that pic of the portal, that's pretty close to how I'd imagine the Dwemer would have built theirs "under the influence", as it were. Interesting pic of the Tower of Babel, btw...Dwemer architecture does have some Persian-esque influences according to some people, and Babylonian architecture was a precursor to Persian.
As for parallels with the story, I wonder if the Et'ada's power was supposed to reach beyond the boundaries of Nirn according to lore, or if the lore is silent about that...That account of the last Dwarf escaping the Dwemer holocaust makes me wonder. I don't know how well the community would respond to it, but you could always hint at a separate set of deities that rule the Outer Realms and use that as the crux of the backstory. Someone a little more knowledgeable could probably tell us if there are even supposed to be any deities specific to the Outer Realms according to lore. Anyway, maybe the deity who ruled that particular plane went mad and destroyed its original inhabitants (if you decide you want to use the alien culture idea), and was thoroughly insane by the time the Dwemer got there, which could explain why they started to go yumpy. Or maybe the deities of the Outer Realms are just so alien that the Dwemer were unwittingly subverted and driven to insanity because they didn't really belong there, and some deity decided to manifest itself within the very metal and stonework of the tower...to become the tower itself. A bit of an ante-up on the original living tower idea, but it could still work. Who's to say that the deities of the Outer Realms would be truly aware of any individual being from Nirn that sets foot in the Outer Realms, or that they would even be sentient in the same way as the Et'ada? Even though, I'm not that clear on exactly how the Aedra are supposed to be sentient.
One last idea for now, and I think this is my personal favorite despite the fact that it's a complete departure from the standard Elder Scrolls mythology archetype: The Outer Realm deities could be Gaia-esque amalgams of all the living things in their planes of existence, like spiritual super-organisms. This does have a certain appeal to me, since it really sets the Outer Realms completely apart from Nirn. The Dwemer could have been driven mad as they slowly became absorbed into the collective "life force" of their particular plane and started to become aware of the collective memories of all the things that had ever lived there. Their lack of understanding of what was happening to them and the hallucinations and delusions that probably would have caused would certainly explain their paranoia and their need to defend themselves from their own phantasms by settings traps everywhere. Perhaps the reason that the tower seems to manifest its living qualities is because of a sort of spiritual echo or imprint left behind when the Dwemer were finally destroyed by their madness, which has been sustained by the collective "memory" of the deity super-organism of that plane. As a matter of act, you could even suggest that the reason that the plane is a barren wasteland is because the Dwemer's alien presence disrupted the balance of nature so badly that when they were destroyed, everything else went with it. Normally you'd think that the removal of the Dwemer would tend to let things eventually rebalance themselves, but the whole idea is that things don't work by the usual set of rules in the Outer Realms.
Well that's enough brainstorming for one night. Besides, I think I'd better stop before I burst a blood vessel .