What is wrong to import the gb roms as a new platform?
Just scrape them as gb. Now you can set up your emulator and everything is fine. I copy all roms over with sgb enhancement cause that are a few mb and dont hurt my storage plus i have a clean sgb enhanced gb collection. You can also use your existing gb roms folder but just i said we talk about a few mb.
Is the double search entry that big problem?
I think you will always have that problem when you use one version of a game with two platforms.
Just think about ps1 games on a ps2. Sensless but possible.
Maybe someone else have a better solution.