"Don't play stupid, don't play dumb / Vagina's where you're really from" marginalizes trans women? Or is it inclusive of trans men? What about trans women with vaginas? What about spiritual vaginas? Whatever, this argument seems like a stretch.

Yes, we should strive to be more inclusive, but every turn of a phrase doesn't have to be welcoming. Like it's written in the article, PR intended this to be abrasive and in-your-face. The criticism seems like a huge nitpick.

"...in essentializing the vagina, Pussy Riot's cis-sexist feminist rhetoric (perhaps inadvertently) excludes trans women."

How do you know they're not saying that we're all born from vagina? I mean, I don't know that they are, since I don't know the rest of the song and all of their oeuvre, but to assume they marginalized transwomen from this one sentence of lyrics is questionable logic.

You must be very young.