I've spent hours trying to figure out which version of Ys Eternal/Complete came with a CD containing official emulations of Ys I-V... no wonder I didn't find it XD
(And no wonder I thought I already had it!)

Freelance writer, somehow
Runs the ridiculously named kimimithegameeatingshemonster.com
Will play just about any game from anywhere and anywhen
https://kimimithegameeatingshemonster.com
https://ko-fi.com/kimimi
I've spent hours trying to figure out which version of Ys Eternal/Complete came with a CD containing official emulations of Ys I-V... no wonder I didn't find it XD
(And no wonder I thought I already had it!)
Oh wow, I somehow never realized 6 came with that collection and it says it right there on the obi for my DVD edition, ahaha. I literally only grabbed it several months ago because it was cheap and "wow, Falcom game in big box," ahaha. So it's not just you, I promise!!! 
Which Ys IV is on the disc? The unremarkable Super NES game, or the TurboDuo game that's vastly superior but somehow isn't regarded as canon?
(Fun fact: I contributed a few voices to the English dub that came out about twelve years ago. Also, it's been twelve years already? Holy shit.)
It's the SNES version of IV, I assume for the reasons you mentioned.
(And the non-Expert version of V)