How do you not even know if your own game was released at all? I remember hearing about the same stuff with Cave shmups, where stuff like Deathsmiles or DoDonPachi DaiFukkatsu have weird obscure versions that were basically never released.
Sadly, until recently there wasn't a big effort made in terms of game preservation, or re-release of older games, and things just end up getting lost. Everything, from games, promotional materials, and even... release information.
Many games are effectively lost (source code long gone, with no backups), there's barely anyone from the old Taito arcade division still around, and the fact that Taito was bought up several times doesn't help either, since many things end up being thrown away.
And it still happens. I was reading a twitter post by Yuzo Koshiro earlier this week, in which he was saying he lost the original recordings he made for the Castlevania: Portrait of Ruin soundtrack, including backups, and that's a 2006 game, just 15 years old.
So, while it seems weird, indeed sometimes it's nearly impossible to get info, or some "obscure" game versions, on older titles.
Additionally, arcade games had frequently multiple arcade "revisions", and alternate versions.
Some were official, despite being rare/obscure, and not normally available (caravan versions for competitions; boss rush versions; alternate versions made for contests, fan conventions, ...). Some are essentially bootlegs, versions made by third parties to change things around, change difficulty, add weird stuff (for example Street Fighter 2 has an insane number of bootleg versions, that did the craziest stuff, and some were so widespread people thought they were official). And there's even "bootlegs" that were done by someone that actually worked on the developing team, who decided, on a non-official capacity, to just mess with the game, and make changes. There's plenty of Cave "weird" versions (or "romhacks", as they are sometimes called) done by someone from the developing team, but were not "official".
Anyway, back to Darius. There's a popular alternate version of Darius Gaiden, usually called "extra version", that everyone thought it was official, but apparently it's not. Considering the extensive changes, maybe it was done by someone from Taito, but this version ended up being excluded from the compilation because it was confirmed as not "official".
On the opposite side, this version you mention of Sagaia was found while M2 was searching for source codes/materials, it's apparently "official", but there was no information, or proof, that it ended up being released. No arcade cabs were found for it, and not even Roms of it were previously available/emutated for MAME, so essentially this is the first time this version was made available, but no one knows exactly what's the story behind it.