Theory1 indicates “The Ami we met isn’t the same demon Ami we have now” and I have no personal beef with it. In fact, brainstorming when the incursion takes place is a lot easier than contemplating on just how perfect Ami Prime's disguise is since the beginning.
Theory2 sounds interesting but that’s the “more convincing” I’d like Selly to push out at some point; not just the goal she tries to achieve, but also “why” letting things happen in a certain way achieves that goal. "I must cockblock my classmates when my uncle invites them over, but I must do it nicely by playing along and I must not cockblock them more than once unless it's Noriko. I will also be Makoto's personal therapist even though her glasses are stupid and I will also pretend I don't know what's happening during reset2. If I do everything right, I will not need to hide myself any longer because Maya one day will be gone inexplicably and Sensei will be back on Ami route". I know I made it sound unnecessary absurd but I need this kind of convincing in good leg works if Selly is to prove that he has a hidden villain well planted since the beginning.
Well, imagine Ami does know from the beginning; At this point it's just Groundhog Day but with horny teenagers and a space war.
If Ami knows doing A leads to B, B leads to C, and C leads to D...her following a specific path makes sense. She also seems to be the trigger for the resets post Maya prime going pop, WHICH Ami is also kinda the cause of. She dressed up as Maya, she cockblocked Sensei a few times, blah blah, she kinda made it to where they would definitely break the rules and fuck in the end, thus killing off Maya Prime.
Add in the boxes in Maya's room, which we now know were being left there by Ami, which Maya would have Sensei's help taking to the school for unknown reasons, it definitely seems like Ami was pushing Sensei and Maya together. Likely because she realized this is the REAL Akira(The one she wants), and she needs Maya out of the way to do so.
The hints are there, and they go pretty far back, BUT, that's not concrete evidence for Ami always knowing. It could just as much be that this version of Ami shows up when Akira prime shows up as well, which would point to my first theory just as much as the second.