So Nintendo Puzzle Collection on the Gamecube does include this - it featured Panel De Pon (Just without the 64), a port of Dr. Mario 64, and a new version of Yoshi's Cookie.
With this, I do wonder if Yoshi's Cookie on this collection was also intended for the N64. I imagine so, but I wonder why Panel De Pon (As Pokemon Puzzle League) and Dr. Mario only came out this way.
Yoshi's Cookie was not a port, it was a native GCN title developed by Tose (even a cursory glance is enough to give away that it's a native GCN game as it's the only one that has native 480p resolution graphics).
Nintendo Puzzle Collection is a very odd product; it seems like it was basically an excuse to release two cancelled N64 titles (though mainly PDP 64) and they commissioned Tose to whip up a new version of Yoshi's Cookie to boost the value of the package as a whole.
Intelligent Systems clearly have a soft spot for the series and the staff were likely very unhappy to have their pet project cancelled on them and bowdlerised yet again! So this was likely an olive branch to placate the staff. PDP 64 was also a significant project for IS as they were
hugely struggling to make the transition to developing 3D games. Remember that they were still primarily making SNES games as a studio all the way up until 2000! Paper Mario was their first 3D game, and it wasn't even true 3D in the traditional sense (IS' first game with fully 3D graphics wouldn't happen until 2005, when they finally released Fire Emblem: Path of Radiance; they were the last Nintendo studio to make the jump to 3D!).
Mind you though, this kind of forward port is VERY much standard fare for Nintendo. Almost ALL of Nintendo's early GCN titles started out on N64 dev kits in some form or another, and many of the titles they did eventually release (and didn't release) were originally planned for the N64. Same thing happened with the Wii, where pretty much every game released within the first two years of that console's life were originally built for GameCube (Fire Emblem Radiant Dawn was such an incredibly last minute GCN-Wii port that the GCN builds were the public face of the game right up until less than two months before launch! Every single piece of pre-release press material was actually taken from a GCN build!). The western release was actually quite a significant overhaul that was a MUCH more polished product and a native Wii title in a way that the Japanese release was not; with substantially improved visuals that were retooled for 16:9 (the original JPN version was 4:3 only).
Nintendo LOVE revisiting cancelled releases and prototypes... Nintendo Labo is a fantastic example; as it is basically a collection of cancelled Wii and Wii U prototypes (that's the real reason why they made it in the first place; they really didn't want their prototypes to go to waste!)
If there's one thing that has always been consistent about Nintendo, it's that they never let good ideas, good prototypes and good assets go to waste. They ALWAYS turn up eventually, even if it's not until 25 years+ later!
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