Correct me if I'm wrong, but doesn't the majority of income for bands come from touring? With the rise of teh interwebs in the last decade or so leading to many people illegally downloading albums, I would suspect that this is the case. However, I know little to nothing about the music industry, so I might be very incorrect.
I do agree with you to an extent, as I consider only three songs from Divine Wings (Accolade, the title track, and Candlelight Fantasia) to be amongst the band's best material. However, I suspect that the majority of Symphony X fans think tracks 5 through 7 (Pharaoh, Eyes of Medusa, Witching Hour) are the most "filler" from Divine Wings, with Medusa being the least filler. I've never considered Out of the Ashes a filler song; to me, it's a short, fun neoclassical romp that serves as a nice bridge between the heavy Sea of Lies and the proggy, drawn-out Accolade. It's a great live song due to its length; it's so short it can literally be squeezed almost anywhere into a set.
This brings me to another point - what songs the band plays live determines what songs they think are filler. For example, has the band ever played Pharaoh or Witching Hour live? Nope. Relic, Orion, Lady of the Snow? Nope. Absence of Light, Fool's Paradise? Nope. The Turning? Nope. Seven or Sacrifice? Nope. I'm not saying that you have to agree with what the band thinks is filler, but this is a good explanation, is it not? Oh, and I left out Rediscovery because it's obviously not filler, but the band probably doesn't want to spend 12 minutes on a song that would make no sense unless the rest of the album came before it.