Well..... Fender's view, and legal issues aside, its a matter of personal taste.
I can buy, engine cases, jugs, heads, crank, pistons, intake, exhaust, igntion, frame, tank, fenders, seat, controls, suspension, wheels, brakes and tires... none of which is "Harley Davidson", and build a Harley. There are folks that do that all the time. And they put the HD logo on the tank, and HD logo'd trim work on things, etc.
You can do the same with old Ford Roadsters, and a few other classic hot rod cars. And they put FORD on the trim.
The question is - WHY?
Do they want to pass of their creation as an actual Fender or Ford product? No. So then why?
The answer is - Because it belongs there. Its part of the look, the charm, the elegance, the overall visual appeal of the final creation. Its an attention to detail. Its an homage to the original originators. Its a superficial, yet important visual cue that makes the final creation visually viable. In short its the nipple at the end of the boob, the cherry on the sundae.
I'm not in favor favor of ripping off folks by trying to remake some clone of a vintage instrument. Or by making an instrument out of the cheapest crap possible and passing it off as quality by way of "the sticker". However, no Warmoth replacement part, if assembled into a whole guitar would ever pass as the Fender product. Many of the parts W makes are BETTER than what Fender provides, in terms of wood, color, finish, options etc.
I dont see the big deal, unless you're trying to rip off somebody, or make a cottage business out of selling the logo itself. Fender does, by the way, provide the logo decal, for a small fee. Available through dealers for replacement on refin. See you're authorized Fender dealer.