Doubt the intonation issues if you want.
I heard it from a well respected guitar tech who said he hated to see warmoth necks come in the door as they were often off and the owners wouldn't/couldn't believe it.
Here's a story where a neck had to be redrilled as to fix an intonation issue.
I'm no setup expert and was merely passing along info I had heard from a respected source.
There's something to be said for a body and neck coming from the same place. Probably be OK if everything lines up...if not could be trouble.
http://www.tdpri.com/forum/archive/inde ... 12563.html