It's great to hear you enjoyed some part of it, I apologise if some things weren't as clear as they should have been. Hopefully, this helps clarify:
For what Telwas wants to do, I'll let you do the side B ending for the details of what his actual plan is, but his broad objective is to limit the influence on the now-stabilising chimeras (including Iustirho) on the rest of the world by confining them to the city of Ledra.
For Iustirho's actual decision - it's informed by both the odd messages he gets from the "other" Zasaroja and the growing connection that is showing itself as they slowly become stable as a chimera, combined with his remaining distrust and dislike of both Telwas and her - he would prefer if Telwas actually could stop Zasaroja, but doesn't trust his capability to do so and is wary of what his actual part in it will be. Similarly, while he doesn't particularly want Zasaroja to succeed, he knows that he probably does have the best chance of survival if he follows her.
Although he doesn't know all the details when actually making the decision, it ends up coming down to being able to live in a world thrown into chaos by five chimeras roaming freely through it or keeping things stable at the cost of being imprisoned indefinitely.
Finally, the drowning scene and the sequence ascending the tower and fighting the various human characters and chimeras didn't physically happen; it was basically a hallucination that occurred as Iustirho and Zasaroja became a stable chimera, representing the final stages of the process - Zasaroja was basically speeding the process of consolidation up through it, whereas in the other ending with Telwas it occurs more slowly on its own while Iustirho and Zasaroja are further away from each other.
The other human characters are entirely dreamt up in that sequence (which is why they either don't speak or are shown suddenly changing languages - the line of dialogue around encountering Ayreen is also in the wrong colour, remembered from a prior scene and shown with no nametag), but the other chimeras and Zasaroja are actually them, speaking to Iustirho in this dreamlike state. The scene after this with Aztargal and Zasaroja also shows Iustirho on the ground in the same place wearing the same clothes as before the whole set of scenes occurred - he and Zasaroja were actually just unconscious on the ground the whole time.
Hopefully that helps - please let me know if you have any further questions either now or after the Side B ending.