If they had the drying stage down right they wouldn't insist on the neck having a hard finish or invalidating the warranty. They also wouldn't be able to crank necks out at the rate they clearly do.
That said, they do a decent enough job that once you pair it with that ridiculous double truss rod of theirs, that thing ain't gonna shift for years. It's a different route, but the end result is the same.
That said.
If a guitar does not appear to hold tune well, I would suggest user error before all else. I've had ''awful'' £80 Strat copies pass through my hands which, after being set up and restrung properly, wouldn't go out of tune for anything but the most absurd vibrato antics. Nine times out of ten—more like nineteen time sout of twenty, really—when somebody turns up with a guitar which they swear has a dodgy bridge/truss rod/nut/tuners, the probably actually turns out to be they were restringing the guitar like a blind chimp.
First up, I strongly recommend you give Ernie Ball titanium coated strings a shot. They don't need as much stretching out when they're new and they don't stretch out as much over their lifetime, either. It helps they also last a long time. I've yet to find a string which stays in tune better.
Second, clean your guitars and make sure any contact points of moving parts are free of flash, burrs, fibres or anything else. It's easy to overlook small specks when you're focused on putting a whole guitar together, but it's those small specks which can throw your 3rd string a quarter step sharp in an instant.
Third, make sure you're restringing the guitar correctly. That means stretching the strings, steaming them if possible, giving them time to relax out of the pack, knotting them at the posts correctly, giving them another stretch once they're on the guitar and putting them through their paces well before it's time to get on stage.
Also consider changing string gauge for different bridge and headstock styles. People often only think about string gauges when they talk about tunings and scale length, but the style of bridge you have and whether the headstock is tilted or not can have a dramatic effect on the feel of the strings when bending and the general tuning stability. It's why tune-o-matic and string-through is a pain in the arse and tune-o-matic and stopbar is pretty faultless and why we have things like string retainer bars for Floyd Rose locking nuts (yes, even though the string is ''locked'').
Broadly, the greater the angle of the strings breaking over the nut, the better the guitar will hold tune, and vice-versa for the bridge (up to a point; you don't want the strings just coming across the saddles completely horizontal). It may be that the Fender body you're using has a bridge with slightly lower profile saddles or some such, so the angle there is shallower and thus tuning is a little more stable.
My advice to anyone with tuning issues is to look at the nut break angle and bridge and if the strings come across the nut fairly flat and the bridge quite steeply (common Fender style), try using strings half a gauge thicker (e.g. .105 instead of .10). They won't feel or sound too different, but they can be more stable. For a steeper break over the nut and a shallower break at the saddles (common Gibson set up), try using strings half a gauge lighter.