I have a slightly weird approach, but it's born of long experience and dictated by efficiency. And that is, I immediately do the fret ends, and if there's any real problem with a high fret. Which with Warmoth was exactly one time in a dozen necks? Several years back they had problems, all on 23rd and 24th frets of seven-string or extended necks. I'm assuming the standard process was used up till the 22nd fret and the last two were done differently - anyway, it went away, the fixed it.
I'm a real fanatic for good fretwork, I've been rolling my own for... dang. 25 years? BUT: I also know that a new neck needs to settle in for a while, it's going to bend itself and flex itself around for a while. So if the frets are reasonably well-seated, as has overwhelmingly been the case with Warmoth & USACG, I just do the fret ends and hold off on the level/crown/polish for at least a few season's changes. Preferably a year. I prefer action a good bit higher than Maximum Shreddy does, which helps.
When I see a company advertising that they "plek" their brand new necks, it seems screwy, because in a year that neck is going to have"matured" and the frets will no longer be as great as could be. It would make more sense to me to include a certificate for Plek'ing so you could have it done after the neck pulls into shape. But of course that would imply that their brand-new baby isn't exactly perfect in every which way, which they ain't a-gonna do.
It's largely a minor issue, because as mentioned above most people don't really care about having a guitar with superb action. And it's probably only a matter of five thousandths of an inch here, seven thousandths there, BUT - if you're doing fretwork, the real stuff, you better be able to think, see and work to tolerances of one-to-two of thousandths of an inch. You kinda have to train your brain to crawl down through a 10X jeweler's loupe and think small for a while.