Sorry for being a tad late to this party, the last storm blew-out interweb access for a day and a half.
You're virtually stuck (no pun intended) with the wet glue method & some visible overlap. Ideally, weatherstrip adhesive would be applied like any other contact cement...allowed to set-up, then the parts assembled. That'd give OEM-like results, i.e. a strong bond and instantly at that. But, you'd have to get the boot in correctly in one shot and that's not likely. If Honda assembled them this way, they had dedicated machinery, which is beyond impractical for anyone else; and they left visible excess glue. That excess adds some strength & durability.
It's not necessary, or desirable, to scuff the visible side. It just needs to be clean & oil-free. If you want to be really perfectionist about this, use a hybrid wet/dry application and mask the painted surface. Start by masking the airbox, leaving a tiny margin around the circumference of the boot. A second layer of masking can be cut from aluminum foil which is guaranteed to withstand the solvents in the adhesive, then peeled-off hours, or day, later. Give the airbox opening a light coating of adhesive, inside & out, as well as the inner lip of the rubber boot. Let them dry, then apply a second layer of adhesive and assemble quickly, while it's still wet enough to allow some wiggle room...literally. Give it a day, or two, to fully set. If you decide to use the dual-layer masking method, the foil can be removed as soon as you've wiped-away most of the excess, using solvent (carefully), to clean the rubber boot. Leave the tape for the next day, that way, there's no chance of any wet glue ending up on the paint. You may have to use a single-edge blade to cleanly break the bond from the tape...hopefully not.
FYI, weatherstrip adhesive will develop good bond strength, even when applied wet. Ever see how tightly the cap will eventually bond to the tube? The key is time...applied wet, it takes far longer.