So here's the thing with Warmoth... if you buy one of the "in-stock" necks, you'll save a considerable chunk of change, but most of those will already be pre- drilled for a Strat. If you have them build you one from scratch, you can opt to not pre-drill for the mounting bolts, but not only is there an up-charge for not drilling the holes, the whole thing will probably end up costing ~25% more than one they've already built, and it's a much longer wait.
Fortunately, it doesn't really matter. You can buy a neck that's already been pre-drilled for Strat mounting bolts. Only one hole is offset on the Variax body... the other three will line up just fine. So that one hole will have to be doweled and re-drilled (it's too close to just drill a new hole and leave the existing one) but this quite simple to do, and even if you don't trust yourself to do it, any competent local tech/ luthier can do it in their sleep, and it's not expensive... you'll spend less money doing this than the extra $ it'll cost you to build one from the ground up.
Either way you choose to go, Warmoth makes great stuff. I'm not affiliated with them in any way...but I've had probably 5 or 6 of their necks on various guitars over the years. I've also built both Strat and Tele "parts-casters" from Warmoth necks and bodies, and they're two of my favorite guitars. As far as I'm concerned, they do Fender better and prettier than Fender does, and for 30-50% less money depending on how figured/ exotic the piece wood, the finish you choose, etc etc.