there has always been regular and limited edition versions of soundtracks for Final Fantasy. Marketing!

Also the theme song most likely needs special agreements to appear on another label's music release as it was most likely handled by an outside source than the Square Enix Music label, as the artist is not an in house artist. Hence why it is not on the XVI soundtrack.

In addition, it was split over 7/8 CD's because of the sheer number of tracks involved. Blu-ray disc was considered but Soken nixed the idea because producing a blu-ray disc involves creating video assets as well as the usual audio stuff and between doing XVI AND XIV he just does not have the time to do it.