Is it true that unless they are featuring a whole album they never choose a song where Portnoy wrote the lyrics?
No, that's not true. They played TROAE on the ADTOE tour and TSF on the DT12 tour.
They've played tons of songs with MP lyrics.
They played The Root of All Evil, War Inside My Head and The Test That Stumped Them All on the ADTOE tour.
They played Strange Deja Vu, Finally Free, The Mirror and The Shattered Fortress on the DT12 tour.
They played Constant Motion, Burning My Soul and parts of A Change of Seasons on the 30th Anniversary tour
The played all of A Change of Seasons on the I&W and Beyond tour (while they played an entire album on that tour, ACOS isn't from that album).