Let me start from saying - if you feel you need professional psychological help, you should get that and not wait for responses here. Take care of yourself.
With that out of the way
--- MASSIVE SPOILERS AHEAD ---
About the flatmates - Marco, his friends, and the random people he was supposed to live with are all foreign students. It isn't said, where they're from, but they are in Rome for only one exchange semester. Marco says that probably no one had the chance to move in after he disappeared, since the police would have closed the apartment for investigation. Plus, the semester is over, and the they had all left Italy already.
About the Parents - they're not evil, at least not like the Other is. But they need the galactic integration to happen and they don't seem to have as much time as they did, when Meera and (to an extent) Drusus failed to help the Galaxias to ascend 10000 years ago. It's not weird for Amicus and Marco to believe that the Parents will let them have a happy future, if they follow the plan. Sure, they have doubts, but they are multiplied by the Other, because it wants them to fail, not because they are sure the Parents can’t be trusted.
Also, after the big fight halfway through, Amicus does everything he can to respect Marco's right to decide his fate for himself. The Parents left Amicus with basically no other choice than to submit, and he doesn't want that for Marco. But he thinks, despite what happened, that their best chance for a happy future is to follow the Parents’ directions. Especially since he knows that they are incredibly powerful and can protect them, so that they can unite the Galaxias.
So why would he ask you to stay. The Parents promised that they’ll have over 200 happy years together after they do what they’re told for a few years. You don’t have that promise, if Marco refuses.
Of course, this is my take, and Khemia, the sequel, might change some things, but for now Amicus and Marco should be fine and have a happy future to look forward to. If you didn't get the vision of Marco's and Amicus' future near the end you should see it (you have to answer positively to all of the choices). It's way more hopeful than the other ending.