I think he means that TC's like the ones here and on GW have easy access to Taylor, and thus will obviously be compatible with PXO. He's wondering how the more "freewheeling" TC's (Ones not on GW or HLP) will fare when the new PXO code comes out.
Code wise there is nothing specific about any mod or TC, the tracker code is totally generic. The only thing that is mod/TC specific is the mission and table CRCs needed to validate against. But all that takes is getting me either the CRCs or the files in question and I'll add them to the database.
Server side there is some mod specific stuff going on though. The TCs (the main ones at least) are getting their own daemon to run with. That means that the people who are available on that server are going to be using that particular TC. There are already 4 different daemons running, including the default one that is open to everybody (though there is no technical restriction on the other daemons). A mod or TC getting their own daemon does require a bit more effort on the part of that particular mod/TC, since you deffinitely have to prove that you warrant such a thing. It's not only extra setup and maintenance for MatthewPapa and myself, but it also requires more server resources (memory, disk space, cpu time, etc). But that proof doesn't require a huge multiplayer contingent for that TC, just a very active one, and one that will actually get some true benefit from the separate server.