That has to do with supply and demand. If Fender sold replacement necks(like they sell replacement pickups) They'd be comparably priced with AllParts, just like their replacement pickups are comparably priced(You can get a J-set from Fender or Dimarzio for about $100, Fender is a few $ more).
Fender used to sell replacement necks. They were very expensive compared to everything else. They were good necks but did not delineate between Jazz and Precision basses.
As for the Fender logo thing:
I've had two things that I've sold with the Fender logo that weren't Fenders. One was a fretless ebony jazz neck modelled after an early 60s Fender neck. It had a Fender logo on the headstock and didn't look anything like the actual Fender one. It was clear coated on and looked fake. (The font was too big and the slightly the wrong style, and the lettering looked cheesy)
The other was a replica 1958 P-bass made from Fender parts. The builder put a Fender logo on it, or maybe the previous owner did. It looked like the real thing from 3 feet away. I disclosed that it was a copy. I didn't like the fact that it had a fake neck plate saying it was a 58 nor did I like the fact that it had a fake date stamp in the neck pocket.
I own an old vintage P-bass with a July 62 Fender jazz neck on it. The restorer applied a period correct Fender P-bass logo to complete the look. I don't have a problem with it. Everything but the pickup is a Fender part.
I own a parts P-bass made from a bunch of Fender USA parts and a JV series neck that was stripped and refretted with brass frets. I wanted a logo for it and at the time I could only get a Fender styled logo. I thought it looked sort of weird without a logo and I figured that it'd look weird without it. If people ask, its a parts bass. Its all Fender parts, with the exception of the neck (even though it was manufactured by Fender) so I didn't see a problem putting a decal on that either.
I also currently own 3 other parts basses.
One is a custom jazz with a warmoth neck. Nothing on it is Fender so it has a flying monkey decal from the Wizard of Oz.
I own a FrankenFender jazz. Really the only Fender part is the body and some hardware. The neck is from a VM Squier. The other parts are, arguably, better than Fender components (audere preamp, vintage spec pickups, high mass bridge, etc) When I got it, it had a Fender logo that wasn't clear coated on to it. It fell off most of the way. I haven't had a desire to replace it. The Squier logo and s/n are on the back of the headstock.
I own another parts P-bass currently being built. I got a second JV series neck for cheap ($20 on CL) and I put that on an American Fender body I had stripped natural. The bridge and strap buttons are Fender but none of the other parts are. My friends are making the bass a collage of their artwork. Each person, including myself, is painting a section of the bass. I plan on painting the headstock with a giant eye with the pupil being the string retainer.I have no plans on putting a Fender decal on it.
I have a problem with people putting a Fender decal on a bass thats just a parts bass without any Fender parts in it, or is just a run of the mill Squier with a changed logo. As long as it is disclosed however, I've had no problem buying basses that aren't Fenders with Fender decals.