When I first read the PW post, I was skeptical for many reasons. I often feel that writers exploit book challenges for publicity purposes, and this had that same feeling. It also seemed unlikely to me that a YA book with five POVs couldn't have a gay teen among the characters. I'd almost expect it -- that's the way teen dramas are on TV too.
I'm not sure I believe the agents either. Agents ARE gatekeepers, as has been said, and as someone who has had the gate slammed, I don't trust them to do the gatekeeping. I'm certain they eliminate books from consideration that editors might publish, just as editors may not publish books that readers might buy. Then again, you can't make readers buy anything they don't want to read. YA readers seem to enjoy reading about gorgeous rich kids, for example, who are certainly overrepresented in teen literature.
ETA: Interesting point about YA lead titles and teen versus adult readers. YA is hot because adults are reading it, and that is shaping what's published because it's what sells.