Nintendo Puzzle Collection is weird. Dr. Mario is a straight port of 64 with the 64 removed from the logo, except not really since DM64 was never released in Japan, making this a new localization? Panel de Pon is the unreleased N64 game, and Yoshi’s Cookie appears to be a completely new version made for this collection. Or maybe the whole thing was an excuse to find some way to release three cancelled N64 projects?
And then it comes with scaled-down versions of all three games that you can transfer to your GBA, except the “scaled down” versions of DM and YC are just the NES versions, while PDP is a new version that was probably used as the basis for actual GBA release that came two years later.