Yes only the seed affects the layout of the universe. But things like AI types and difficulty levels, Hybrids (on/off.. what difficulty level).. affect on AI buildings that are seeded into the universe. Like the position of Raid Engines, AI Eyes, Advanced Factories. It's because AIs can only have X amount of Y on every planet (or something like that). If I'm playing with 5/5 Hybrids the universe will have much more Hybrid Facilities which will take space.. so they affect the seeding of other buildings.
It does impact the seeding of other buildings, but not because of a lack of space or capacity or whatever. It's just because if the game says:
RNG, pick a place for this command station.
RNG, pick a number of fortresses between X and Y.
RNG, pick a place for this Fortress.
in one start, but due to different options says this in another start:
RNG, pick a place for this command station.
RNG, pick a place for this hybrid spawner
RNG, pick a number of fortresses between X and Y.
RNG, pick a place for this Fortress.
Then the number-of-fortress-pick and the fortress-position-pick will get different rolls, despite using the same original seed.