I actually think you have a point here, and this idea has been brought up. Players queuing on both Bastion and POT5 can match up together, but on a seperate, "invisible" game server, where the actual matches take place. As far as what you said about a loss of competition between servers, I disagree.
People have guild tags for many reasons. One of which is to proudly display their allegiance, whether it be a POT5 or BASTION guild.