it all depends on the customer's preferred set-up. the lower and more insane the action, the higher the probability that the neck will not only need to be shimmed but also that the frets will need microscopic detail to their levelling.
I've done a lot of builds and have yet to see an issue with Warmoth body + Warmoth neck, or putting Warmoth neck on American Fender body. I have had to do significant sanding (in lieu of shimming) to get correct neck angle on a couple of Musikraft necks on Warmoth bodies.
if you have properly adjusted the relief on your neck, and have bottomed out your bridges saddles but still have action that is too high ... a properly installed shim may just be the ticket to set-up perfection