It basically comes down to "what does that band consider to be a song?" When the band started writing Metropolis pt 2, yes, they intended it to be just one 21 minute song. But after FII when they started discussing the next album, they decided that the next record should be a concept album, and since they had an incomplete Metropolis sequel left over from FII, they decided that rather then making Metropolis an epic song, they would expand the concept and divide up the existing parts into a whole album. SFAM is one single piece of music throughout, but it is no more a "song" then, say, Beethoven's entire XI Symphony is one big 74 min "song".
On the flip side, when writing the 6DOIT album, the band actually took a break after writing the first 5 tracks to play some shows. After that, when they returned to the studio, they decided to write an epic similar to "A Change of Seasons" (this is actually mentioned both in Lifting Shadows and in the FAQ on MP's website). The fact that the song ended up being 42 minutes long was a result of the band getting into a very creative groove while deliberately trying to make a long song. It was indexed by movement because even Dream Theater recognized that having a single 42 minute track on an album would render the work a bit daunting and inaccessible to the listener. But it was still listed on the album sleeve as a single 42 minute song, and on Score they actually did make it one single track, so I think it should be obvious that the band considers it to be one song consisting of eight movements, no different then "A Change of Seasons" consisting of seven movements.
Ultimately, what constitutes a "song" as opposed to a suite or an album is at the discretion of the creator. I could argue that Symphony X's V is one big 62 minute song (and, not unlike SFAM, V was built around an incomplete 20 minute epic from the previous album), but the band explicitly lists it as a "suite", and they treat the individual songs on it as such. Likewise, I would argue that Fates Warning's A Pleasant Shade of Grey is a concept album, and not a song, but the band has stated that they wrote it as one big 54 minute song, and simply decided to index it by section for the sake of convenience for the listener. This sort of thing is really the decision of the artist, not the listener. The listener may think of the individual parts of 6DOIT or APSOG as "songs", and no one can stop them from doing so, but both bands have stated that they wrote those works as "songs", not "suites", and they consider them to be such. Ultimately, it is the artist, the creator of the work, who decides what makes a "song", a "suite", or an album, not the audience, who simply listens to it and had no hand in it's creation, and therefore is in no position to dictate to the creators of a work what constitutes a "song", "suite" or album.