It's because they have no quality control over the finish, the hardware, etc. that the end user adds. When I bought my Carvin kit it had the same parts Carvin uses but no logo. They don't want their name on my work.
This doesn't really hold up. Fender knows damn well that if someone wants a Fender logo on their Warmoth neck, they will get it, one way or another. Also, people do all kinds of unspeakable things to real Fenders that make them hideous, all the while leaving the Fender name on them.