I've never seen this box layout before. That being said last year around this time I posted some images of early packaging design layouts on Digital Press. One of them was for Sonic Spinball or as it was at that time of development Sonic Pinball.
I always really hated the cover art for the Genesis version, Sonic looks like ass on it. The Game Gear cover is a big improvement But they compensate by making Robotnik uglier and using the AOSTH design, which they kept using in the game art for some reason, like in the Triple Trouble art
SoA (and I'm guessing SoE) started to use that design of Robotnik for all Sonic merchandise and game box art designs a bit after Sonic 3, probably to keep in line with the show. From about 94 to 99, that's what was sadly considered Robotnik, extremely conflicting in game designs be damned.
I always thought it was a bit dumb that they changed the sea to lava in the Spinball box-art. I know, they're trying to make it more dramatic, but it doesn't line up at all. It's not just an aesthetic choice, it's a flat out different material that functions very differently. Given the opening cutscene, that would've been it. Crispy hedgehog, no pinballing, no future.
Yeah but both Stages 2 and 4 have really prominent lava fixtures. The giant gaping maw in the volcano certainly brings to mind the cutscene right after The Machine leading into Showdown God DAMN that is great. Despite the art deco influences on the games' visual design almost none of the other official art actually carries through on it. But that is excellent.
In fact that doesn't look like art Déco si much, it's like some neo-Futurism. You can tell because of the 'trail of movement' sonic has behind him, it's very peculiar and tied to this specific movement. And about it being excellent, the rest is but Sonic's face is just 'ass'cellent. :X
You aren't the first I've heard say that they prefer the game gear box design. You may or may not be surprised to hear that both boxes were illustrated by the same person, Greg Martin.