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--- Again, SPOILERS ---

You should really go back and do the other path. The Meera ending is seriously super bleak in comparison, and I was kinda upset by it too.

But the whole point of the Other is to make sapiens doubt themselves, and the Parents. When you go back you can guess, which characters are influenced by the Other. It even says that it's "always watching, willing you to die." It exposes some real flaws of the Parents, but in the end I wouldn't trust an entity that from the start tried to break Marco with doubt and terrifying visions.

Plus, Marco immediately forgets it, but we know how the amalgamation looks like and we know that "Meera" is lying about it.

Yeah, I'm suspecting it was him, but I think he contacted the other spies in the city and they somehow forced the girl to come up to the MC. She seemed pretty upset, so I think they threatened her. Either way, hope there's an option to yeet Alex into a garbage can in the sequel

--- SPOILER ALERT ----

Again, this changes a lot depending on what happens, when you meet the Monitor for the last time. Depending on your choices, Marco either talks with a new character and gets presented with more doubts (I suspect this is what you got?), or like Amicus, he gets to see their future. The Monitor specifically says that it "is guaranteed if you follow all of our instructions." He shows that Marco and Amicus will not be separated again after those 8 years and will live happily together for around 250 years.

Amicus almost loses Marco twice, after which he is told by the Parents that if they both follow their instructions, that will never happen again. Just like giving up his free will was worth it to save Marco, 8 years apart is worth a lifetime (and more) of happiness.

Something terrible could happen, if Marco decides to stay and not take on the mission. They know that, they've already seen it happen. So when creatures that Amicus was taught to revere, creatures that can see the future, bring back the dead, and change reality tell him that they guarantee they will keep them out of harm's way to allow them to unite the Galaxias (and then enjoy their earned rest), he has little reason not to follow them.

Those 8 years will be hard on both of them (Amicus doesn't really have friends apart from Marco, only political allies), but it's worth it for the life they will have together.

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.

The game doesn't say that Amicus keeps constantly asking you to bottom, just that you had sex many times and he asked just a few times (and then stopped asking). And that the MC did not say he did not want to bottom, just that he's nervous about the size (he says "some other time," and there's nothing in the game to suggest he says that, because he can't say no to Amicus).

Adastra mirrors the sexual norms of our classical antiquity. Gay sex is frowned upon, but bottoming was seen as magnitudes worse than topping. Penetrating someone was about power and societal position. The handful of texts from that time that present gay couples positively religiously follow the rule that the older, more powerful, and more influential partner is the one doing the penetration.

So Amicus grew up in such an atmosphere. Being gay is bad and shameful enough, and he's also aware that he'd probably lose any claim to the throne, if he bottomed and that information got out to the public. So there's that, plus the fact that he just prefers topping, which is perfectly fine. He's also expecting you to say no. So he asks again, but he's mentally preparing to bottom (for the first time, btw). Even if you say yes he says "we don't need to do this at all," when he sees that you're nervous. So he's ready to do anything to be more intimate with you, since you'll be separated soon, but he puts your comfort first. Like during the first time, when he asks "is this okay," he's checking in with you throughout.

As to the second point, I agree with Esuriit. It's not like Amicus just wants to get off, he wants to be intimate with you (and no one else). I don't think there's anything wrong with him desiring you on a physical level. 
The MC is a defined character and I got the feeling it was assumed that a) he's very much on board with the sex, and b) he'd prefer bottoming, but he's nervous, because of the size difference and the fact that he's never done anything before the timeline of the game other than some handjobs.

I don't know, after the fight before the second trial, I got the feeling that Amicus was nothing but considerate and respectful towards the MC.

I was wary to play this, since the story in Echo was incredibly bleak and I couldn't finish it, but a few friends recommended this. And I'm so incredibly happy that I did finally play Adastra.

Once I started, I couldn't stop and finished the game in two days. The setting, the characters, and the story are just so incredibly well written. I can't stop thinking about the plot and about what's coming. Unlike with some other VNs, I did not mind the limited dialogue choices. The main character said and felt exactly as I would. And the art is just beautiful. Haps really gave the designs so much charm and personality.

And Amicus is so amazing. I love him and how the relationship grew. I can't believe how many times I cried. I keep coming back to the final island scene and just start crying every time the music starts playing. There are very few stories, where I got so attached to the characters.

The universe is spherical, can't convince me otherwise.
Thank you for the wonderful experience! Can't wait for Khemia.

P.S. plz Howly don't hurt Amicus and his husband in the sequels, my heart won't be able to take it

--SPOILERS--

I think it's implied that yes, she is the one who gives you "avia pox." And I'm pretty sure someone had planned for this to happen.