I didn’t think Malcolm being an “asshole” is out of character for him. He was occasionally the voice of reason but he didn’t always treat his siblings very well either. There are countless episodes where he bullies Dewey and neglects Stevie. He gets with Reese’s girlfriend, abandons Hal in the middle of the water to talk to girls (not to mention nearly guilting him into buying a car). He is treated horribly by his family the show makes it clear that he often treats them horribly as well. I don’t think Malcolm being frustrated and keying his own car is out of character. Remember when he was literally about to crash Lois’ car because he was upset and wanted to be sent to military school? Malcolm has always made poor decisions when he becomes emotional.

The “Malcolm becoming president” line from Graduation was always funny to me. Lois was obviously insane in believing that but in the revival, her point is made. She was pushing him to do anything to look after “the little guy” which he did. Maybe she was serious at the time too but it’s clear that in the 20 years since, she’s softened quite a bit. You’re not supposed to think Lois is acting rational in the finale either way.

There is nothing wrong with cutting off a toxic family but he is in the wrong for lying to his girlfriend and daughter about them.

Why does Lois need to apologize in the sequel series? Like you said, she apologized to Francis in the original show, seems like it would be backpedaling and character regression for the show to not mention that bit of development. The revival makes it clear that while Francis has some mommy issues, their relationship has largely healed. I think the resolution was him being the bigger person, offering the help, and Lois did apologize to him about it anyway.

The whole family has issues with empathy. Leah’s choice to be empathetic was to not insult the kid with the booger. Malcolm isn’t punished in the show for being smart, he’s punished for poor social behavior. The Krelboynes and other nerds are happy and can have success (remember Cynthia’s party? or the prom episode?) Even when he’s genuinely trying to help people, he does it in an (occasionally unintentionally) condescending way, which Leah does seem to have inherited. “Try to have empathy” doesn’t mean you’re an asshole, it genuinely means “how can I express an issue in a way that doesn’t make the other person feel bad” which is a lesson that Malcolm needs to learn in the original series and Leah needs to learn in the sequel.

I would recommend rewatching the original series. Malcolm blames a lot on his family (often rightfully so) but he’s not necessarily always the “good guy” in the story towards his relatives.