Hmm…I'd try a few different workshops and see what they say – can't why it's not possible to just spot in the missing lacquer – equally, if you're thinking of stripping the finish, do you need to worry about odd chips ?
Pretty sure all maple necks are laquered *after* fretting, not before. Certainly a refret job requires the lacquer to be stripped to be done properly.
>need to be stripped, have the frets removed
Might be how you've written it, sounds the wrong way round to me – stripping it ought to be easier once the frets are off (otherwise they're doing the job you wanted done, first, anyway)
I guess with a scalloped neck there's not much finger<>fretboard contact. I guess there's a couple of reasons they're lacquered is – mebbe gives it a harder finish, maple's gona pick up marks and stains unlike rosewood (or at least, you'll see 'em) And you'd use (lemon) oil on a rose wood neck to stop it drying out. Dunno if neck stability is affected at all – might make it more vulnerable to short-term changes in humidity.
Might be worth mentioning to Fender UK to see what they say – I guess it's out of warranty but they may have a view..