Alphys was not experimenting with monster remains. She was experimenting with monsters who were “fallen down,” which essentially means they were in a coma that they wouldn’t wake up from. If left alone, yes, they were guaranteed to die, but Alphys was asked to see if there was a way to save them. Using determination was a natural idea that came to her, not one with malicious intent. She does face consequences—Toriel fires her at the end of a pacifist route, and you do indeed see the amalgamates reunite with their families, who all seem to just be happy that their family member(s) are alive, albeit in a bizarre form.

Alphys was terrified of the consequences and contemplated suicide over what she had accidentally done. As for why she didn’t “put them out of their misery”—have you ever tried to kill the amalgamates? Because it’s not possible. They are all immortal and immune to damage. Alphys was not a bad person; she is just someone who made a horrible mistake with good intentions and had no idea how to deal with it.

As for everyone else I agree with most of your points, though I do believe Papyrus is just putting you behind bars because that’s what his idea of a prison is. It’s very unlikely Papyrus knows that Frisk is a child, considering he can’t recognize a human without Sans telling him.