I use real sticker paper for printing genesis and snes labels but if I didn't, I'd use spray adhesive. It should work better and if it's sprayed evenly, you shouldn't see any bumps. Should be like a real sticker. The BL label is the one that caught my attention as looking uneven or warped.

What specific paper are you using? There aren't too many options for high quality adhesive-baked paper for consumer use, so I'm curious.
I love spray adhesive as much as the next guy, but for it to be permanent BOTH the paper and cart would need to be sprayed. In my opinion, this sort of thing is too small and tedious for something as sloppy as a spray adhesive. Plus there's just no need for the extra mess that it causes.
Well, you're wrong about the surface, I don't know what else to tell you. The bumps that you see are the same that you'll see in an OEM label. It has NOTHING to do with the adhesive that I use. It's just the nature of the material used and there's really no way around it unless you want to laminate the damned thing, which would of course make it far too thick and rigid to be of any use.
The texture is virtually identical to an OEM label when placed side by side. The ONLY difference is that my label is brand new, and thus still VERY glossy, which serves to accentuate any surface undulation. Trust me, if you were here holding it in your hand you would just think that it's a fresh from the box SNES game.
Do you have any examples of your labels to show?