"Ys IV" as a whole only exists because Hudson specifically asked Falcom that they wanted "Ys IV" on PC Engine CD, due to the big success of their port of Ys I&II and other Falcom games. But since no PC-x8 version existed, the entire Ys dev team left Falcom in 1989 and the current staff was busy with other games (Brandish 2, The Legend of Xanadu, White Witch, etc), Falcom was not able to make it by themselves and instead Hudson offered to make The Dawn of Ys, with Falcom handling them a rough scenario draft and music (i.e. J.D.K. Special). This is also why the track titles for both J.D.K. Special albums follow The Dawn of Ys' context better than Mask of the Sun's (e.g. Temple of the Sun plays on some random dungeon at the beginning, using Valley of Quicksand on some random forest with thunderstorms, etc), nevermind how both the first J.D.K. Special album and Yonemitsu's Perfect Collection arrange albums use art and logo from Hudson's game. Then Tonkin House also got a license and materials from Falcom at some point and released Mask of the Sun; while Mask of the Sun did release a month earlier, development for The Dawn of Ys started earlier and took nearly two years.
The liner notes of this album (probably written by Jun Endo again) pretty much say that this FM soundtrack is the original version, and if Falcom had released a PC-98 original by themselves, it would have been called "Music from Ys IV" on album. But since no actual game with this version of the soundtrack exists and King Records only used the "Music from~" nomenclature for actual game/anime soundtracks, it got labelled as "J.D.K. Special" instead. Disc 3 of Special Box '95 contains all the remaining tracks that they couldn't include in the standalone 1993 album due to lack of CD space, in addition to a few unused songs; Tower was not arranged for The Dawn of Ys but shows up in Mask of the Sun, and Crater was arranged for Mask of the Sun but went unused.
The cancelled Mega CD version of Ys IV was part of the lineup of Sega and Falcom's short-lived joint venture, along with the also cancelled Super Brandish. Their represented tracks in
TIM-SMD01 are just arrangements taken from
Special Box '93 and
Perfect Collection Brandish respectively, which is rather questionable given that Yonemitsu already fully commited to arrange all the redbook audio for The Dawn of Ys and how unfitting Kishimoto's J.D.K. BAND arranges are for in-game use. I imagine Sega-Falcom just had no pieces of music ready for neither project and simply sent these album arrangements for whether reason.