While good, like with Fire Emblem Fates with that romance option to fix a woman who likes other women (which I'm still surprised Kotaku actually pulled "But censorship" thing on that), I still don't feel comfortable knowing what the creator's intent actually was and knowing no matter what I played, any time I'll go online I'll be reminded of the transphobia from the original version. Don't feel comfortable with playing any Atlus game honestly.
That's basically my take on it.
It's nice that Atlus USA thinks that this kind of thing isn't acceptable, but ultimately all they are doing is masking the original intent of the game for western players. It does nothing to alleviate the LGBT+phobia of the original text in its home country, japanese LGBT+ people still have to put up with it. I'm not necessarily saying that Atlus USA was wrong to do this, but the thing is it still doesn't address the core of the issue and western players' money is still going to transphobes.
Also, to the question of whether Vincent's character being transphobic is authorial intent or not:
You have to take into consideration the whole context of the work to see what the authorial intent is. For example if you watch Mad Men, it is very obvious that the male characters' sexist attitudes are supposed to be intentional character flaws, because of the specific way the scenes are written and staged. If you apply the same analysis to Catherine, it becomes clear that the transphobia isn't meant to be a damning character flaw of Vincent's, rather it represents Hashino and co.'s attitudes towards trans people because of how casual it is. The characters' jokes and transphobic comments are not addressed, challenged or defied by the narrative, they are just presented as is.