I think you have a point. But remember, you don't really need to have large number of songs to play from to play a show. Think about it: How many songs can you pack into an show? The Divine Wings of Tragedy is a little bit over an hour long. Same with The Odyssey.
I went to a DT concert, 3/26/06, the concert was probably about 2 1/2 hours long (of actual music -- also remember, there was no opening act). So a full tour of both of them; no opener/main event, a dual band tour, might each have about 2 hours to themselves. That could easily work.
Symphony X would have to put in a lot of work to really be able to side DT, and I agree that SX would probably not be able to actually headline over DT. I still think a side-by-side tour could definitely work. I really hope it will, at least eventually. I'll be waiting.