So... just a personal side note from me, in honour of the season: stop calling it homophobia and transphobia. They're not scared of queers, they're engaged in hateful acts and dialogue. Racism, I'm led to understand, used to be referred to as a "phobia" prior to someone coining the more appropriate phrases of racism and white supremacy. I recommend "cishet supremacy", personally.
The weird part about these positions is that it's hype poison and it
keeps happening. Even leaving out their growth markets in the West, in Japan (and Asia on the whole, really), you'll see commentary against these awful narrative traits in Atlus' work (less so on the cishet supremacy front and more on the misogyny front, but you
will see both), with that commentary growing more and more as time goes on. So the maintenance of those traits in their work aren't doing Atlus any damn favours and should be addressed quite rapidly.
I know that some folks would only be happy if they pushed Hashino out of Atlus and they're within their right to want that, but, as has been pointed out by
@Mendinso and others, this is a culture issue within Atlus as a whole. That in mind, I personally wouldn't be against Sega stepping in and overruling Atlus creatively on these topics along with some mandatory inclusivity education at Atlus to see if that sticks, at least as a first attempt.