As TCRF wiki states, files played on a Game Boy or Game Boy Colour are incompatible with the other system, with the game refusing to let you play them on the other console:
You're telling me the Game Boy of color is getting seperate save ? Sounds like racial segragation to me.
In all seriousness, if I had to take a uneducated guess, I'd say maybe the developpers didn't want to risk any potential issues that could come up with making the saves able to open by either systems ? But I doubt Wario Land 2 was the first Dual GB/GBC game so.... even my theory doesn't make much sense. Maybe there's something specific in Wario Land 2's coding the other Dual GB/GBC games don't have that may have worried the devs that the game would have issues ?