Indeed, there are tons of multiplatform games where one version is significantly more valuable, just because it's rarer. And the most valuable version is often not the best version.

As far as "collectibility" goes, the original version of a game counts for something, but I see far more people talking about wanting to play "definitive" versions of games, and later versions are often regarded as better in that regard. So the later version sells way more copies, and the older version commands a premium because there are fewer to go around. As for Rondo, the PC Engine version is not only significantly rarer, but it's also a superior version in a number of ways (it's the only proper physical console release, for one; playing a handheld game with TV out just isn't the same). So its price definitely has way more factors involved than it being the original release.