Regarding the whole "can Batman exist in this Gotham?"/"Can Batman still exist if Thomas Wayne was a bad person?" debate:
I think it's fairly ambiguous.
In the late 70's and early 80's Thomas Wayne was occassionally portrayed as a less than engaged, gruff, potentially abusive or neglectful father figure.
There's a story called "To Kill a Legend" from 1981's Detective Comics #500 issue where Batman goes back in time/to an alternative timeline with Robin thanks to The Phantom Stranger, and we meet young Bruce, and he's kind of a spoiled brat. The murder of his parents sets him on a different path, and adult Bruce himself muses about what might have been had his life not gone in that direction. They don't really go there in this movie, but they could if they continued the story.
The movie presents everything with enough ambiguity there's not really any indication that Thomas is truly bad, corrupt, etc. You can interpret it as you see fit.
As for whether the movie glamorizes Joker and his actions...there are some pretty clear context clues to consider. The only time Arthur receives fanfare/applause when he is not engaging in violence are either fantasy/dream type sequences. The other times...who is applauding/praising/looking up to him? A seemingly reckless, violent mob. Consider the source of the praise when assessing what the movie's creators are trying to say about whether his actions are justified.
And look at the shift in Phoenix's performance. When he's misunderstood, downtrodden Arthur Fleck, he generally comes across as socially awkward, but also sort of charismatic, someone potentially likeable, even if
. When he's starting down the path to violence, and Joker? Not even close. He alters his voice, his speech patterns, his mannerisms, he plays up the "monster" in the man, I assume so the audience understands that this isn't to be sympathized with just because he was once a sympathetic figure.