For me, it's just that the way EM is composed, it works with a live energy, but feels a little flat when it does not have that energy. To my ears, EM sounds like jamming music, and the "fun" feeling of the jam is lost in the studio version. Studio instrumentals for me work best if it's composed like a song, like New Millennium, Stream of Consciousness, or Overture 1928.
And yes, I will say that it might work BETTER as a live piece, but that doesn't make it bad as a studio experience. If it's not your thing, it's not your thing. You can skip it. But don't say "the should've just left it off the album all together," like, "If I don't enjoy listening to it on the album, then other people who do enjoy it shouldn't get to listen to it." Personally, until recently, I didn't even listen to live albums. I'd watch the DVDs, sure, but it wasn't until a few months ago, that I really started getting into and enjoying their live albums and bootlegs, and so it was only within the past few months that I got to enjoy stuff like Moon Bubbles or Bombay Vindaloo. Point is, some people just prefer listening to studio material over live material. They shouldn't be deprived of songs as a result.
Besides, all those other instrumentals you mentioned, I'd take The Dance of Eternity over any of them, studio or otherwise, and it's from the same basic camp as Enigma Machine. Wankfest in the best of ways, and I think every DT album needs to have at least one section like that, whether it's a stand alone instrumental like EM, or whether it's in the middle of a song, like with TMOLS.