We definitely share your concerns. It would be ideal if WAX built on the chains governed by the main EOS token. And who knows? They still might. We don't think that forking the EOS.IO repository to build your own blockchain will be a popular route and we aren't saying that EOS New York supports this. We just wanted to help dispel any concern that this was the end of the world.
EOS New York nor any block producer candidate has any influence over what WAX does. Their reasons for creating their own chain were a little vague, but they say they have their reasons.
We also could not confirm the extent that WAX is working with Block.One or if they're working together at all.
It's the goal of EOS New York to spur as much development as possible on the chains that support the main token. We have yet to realize the effect of inter-blockchain communication so we just aren't jumping to negative conclusions just yet.
RE: Why WAX choosing to build their own blockchain based on EOS.IO isn't a bad thing.