Going through my first playthrough of Reborn, when the time finally came for me to choose a split for the Zekrom or Reshiram routes, I personally chose the Reshiram route- after doing a bit of looking around I figured that a more blunt, or "truthful" route of this story fit the dark mood of Reborn more. And, oh boy, did it deliver.
(Apologies if this is the wrong place to say this, as I know this is a discussion about Amaria, but I just wanted to comment:) You pointed out that on your second run of Reborn, your perspective on some of the characters had changed- which I thought was pretty interesting! Two of my favorite characters that you pointed out were Corey, and ironically, Fern (Yes, Fern). As for me, Corey already had a place of sympathy the first time I realized that he had been unmasked as part of Team Meteor in front of his own daughter- and his death was so sad (Yes, I cried-), and yet fitting, I feel. As for Fern, I never really hated him, I just thought he was a jerk but found his little jabs at the MC funny. As you said, there's a sense of insecurity from him, which begs the question as to why? (If his story is ever developed more I do hope it might explain why he acts the way he does), and the moment I saw him on Team Meteor's side, his character just piqued my interest more (that's a topic for some other time, this is about Amaria, not Fern!).
When I finally got to Amaria's gym, the part where she tries to literally drown the MC is certainly shocking, but I suppose you could say in her head, it was very much justified. Titania was the only person she could lean on, the only person who wouldn't leave her, and so obviously she depended on her so much it that Tania had become her lifeline- but it got to the point where it was so much, it was toxic. As you said, Amaria leaves Tania trapped- so it was certainly a tight spot for her to be in. She obviously needs help- professional help- and she wasn't going to get it herself- which just led her to spiral worse and worse until she just becomes unhinged and tries to kill the MC. Personally, Amaria didn't really bother me too much (?), as for the relationship between these two characters, I was more focused on Titania's side, since the idea of someone being trapped in such a difficult spot was interesting to me- as well as her breaking away from Amaria in the Reshiram route. However, even though my opinion on Amaria was typically surface level for most of the story, there is one part that really stung me the wrong way.
It's when you try and find her in her gym, and she says:
"I know- She doesn't love me. I've tasted the disdain on her lips a half-thousand times. I'd suck the venom right from her tongue a half-thousand more if it meant she would always be here..."
The fact that Amaria is so vividly aware that Titania feels trapped in this relationship, and yet still keeps going, is so disturbing to me. For her to be so dependent on Titania and ignore her friend's feelings like that just for herself was really the moment I started to realize that something was really wrong. I wonder if Amaria's love for Titania is really love? Or maybe it's just some sort of twisted kind of dependence on her because she's never had anyone else to lean on.
Either way, Amaria's actions could also be said as justified- her depression leads her to act this way- since she's in such a dark place, so she can't really see the rights and wrongs in her actions. However, I'm not the one to say these things, as I've never really experienced depression (so I hope I didn't come off as ignorant n~n;;), but sympathy for everyone who had to go through it. Yet at the same time, for her to act so selfishly is also shocking, as you would expect her to care more for how Titania feels in the relationship as well- and yet she doesn't. In the end, I would simply say she's acting human- someone who has been through too much, and never really got the help they severely needed, nor did they ever learn to pick themselves up and hold themselves responsible to heal, as you said. Both Titania's and Amaria's stories are sad, as well as so bluntly human. People make mistakes, shy away from standing up to toxic relationships, make the wrong choices, and sometimes even spiral down a painful path because there was never anyone to really help them get up- just like Amaria.
I'm not sure if her actions can ever be justified- but I still think that doesn't take away the fact that the story of these two is so very much human.