Fender guitar necks, as you said, can be licensed for use by other manufacturers to produce replacement necks and bodies.
Fender has trademarked certain headstock shapes, like those of the Stratocaster and Telecaster, and has granted licenses to other companies to use these shapes on replacement necks.
Companies like Mighty Mite, WD, Warmoth, and Allparts manufacture necks under Fender's quality control trademark license, ensuring they meet specific standards of quality and dimension. The licenses bear certain requirements, such as the inclusion of Fender-approved language on the heel of the neck, restrictions on decals or insignias, and adherence to Fender's vintage specifications.
A company called BYOGuitar, never heard of them before quite honestly, also sells Fender-licensed necks.
Now, the necks and bodies that aren't Fender Branded?
Let's say for example, Guitar Fetish necks and bodies.
There's nothing wrong or illegal about using such parts in your build or projects.
There's no legal trouble involved.
It's just considered 'fair play' to declare where you got the parts from when you go to sell the guitar later on.
And though it is very common, it's considered bad form to put a Fender waterslide decal on the headstock, and represent the guitar as a genuine Fender.
Do people do it anyway?
All the time.
