Thanks for the extra context about Twelfth Night! That's actually helpful to know that the Malvolio subplot typically isn't played as comic. And thanks for the rec of the NT at Home version! It sounds very appealing, and I like the idea of Malvolia getting to walk away with pride.

There's also an undeniable shade of queer bashing when you have a female Malvolia

That was definitely one of the undercurrents I got when I was watching. Nothing overt that I can remember the production doing, but it's a real world context you can't help thinking about.

but without cross casting Viola as you observed, the endings are always straight

In the program book, the director talked about how in Shakespeare's day, the all-male cast meant that the ending resulted in a series of male couples. And she wanted to have the dramaturgical effect of an all-male cast without having an all-male cast. (My sister pointed out that it means a leading role for a female actor gets taken instead by a male actor. But I suppose every production can't be everything, and this one is doing one particular thing.)

I think with Malvolio it really matters how the production handles that character.

Yeah, I can imagine it might be worse if what Malvolio went through just got brushed aside lightly. I appreciate that this production treated the character very sympathetically. I think my strong reaction was because of how unexpectedly dark it was, and the specific way they chose to portray it. But I'd be interested to see how other productions have done this story.

that's where I am with Taming of the Shrew

I have vague memories of having watched Kiss Me Kate, but yeah, I don't think I would feel up to watching Taming of the Shrew.