Good point. Although many people's reasoning for that is because Portnoy wrote it, and not because it's never been played, so that's where I stand a little confused.
My main reason for doubting that MP songs will appear in the set is mainly due to the lack of his vocals. Sure JP can do his backing vox but it won't be the same. For that reason i'd probably suggest that stuff like Constant Motion, TDEN, Honor Thy Father, maybe Glass Prison and anything else with an abundance of Portnoy vox probably won't get an outing, at least at first. They could do Nightmare with a guest growler or MM could man up and cookie monster them.
I honestly don't know what they're going to do about other lyrical content that is personal to Portnoy. ACOS barely gets played these days. TBOT is a certainty not to get played (probably ever unless MP returns). I don't know about the AA suite stuff but they probably won't do much of that at first either. Playing stuff really personal to Portnoy would seem a little tasteless and I don't think the other guys have that in them to do that. Songs with lyrical content that Portnoy wrote that isn't personal (Octavarium, New Millenium, his stuff in 6DOIT and his lyrics from Scenes) will probably be candidates to be played.