It can make sense. It works better with proper management if a single console is the home of a group. It worked with GTAV. Admittedly that had member caps, and I am told Destiny groups have no maximum amount of members (besides the alpha) so it is not entirely the same. But GTAV had at least like two ps3 groups and two 360 groups.
Say you have a thread in GAF. If it's all encompassing then people will have to go page after page to make sure they find somebody to add to their friends list, or to play with because there's no assurance their console will be the discussed one in the last couple of pages.
If you do it via the Bungie site then there will have to be either a mega-thread for each console, or many threads per console, thereby making searching around the place for what you need similar. Making console-centric crews/groups is not unheard of, it's a well-known practice and it has been done before in mega forums such as this. It wasn't known to begin with, and still isn't 100% clear, how groups will work in Destiny. Do I get to join them like in GTAV and Halo 2? Or is it simply a community and we get to co-op via our own means?
Again I'm all for joining the two into one, because the beta is most likely a month or two away at the farthest. But let's not pretend it doesn't make sense, when it has been done before. Mistake or not, it is already done and there is a sizable amount of people joining both. Nobody did it out of spite.