I've always seen the Warmoth guitar I built as a tribute to the Stratocaster as originally made by Fender. Not the strat-ish S-model copycaster, but the Fender Stratocaster, which is why I put a "Fender Stratocaster" decal on it.
It's really hard to find a better argument than "It completes the look" when I see no reason why a guy can't do whatever he wants to his custom guitar.
Supposing I died, got robbed, or fell on hard times and had to sell the guitar (forgetting that I had put it together) there are enough differences between my Warmoth and a genuine Fender for someone who's been to a guitar store (not just a guitar nerd) to tell what it is. Besides the side truss rod adjuster, the fretboards on Warmoth necks are cut a lot thicker than on Fenders (new or old). And you wouldn't have to be a remarkably keen observer to spot the neck's hard U shaped heel, which is not what Fender typically does there (in any of their series). And if you were still in doubt, just pop the neck off. Warmoth and the other reputable Fender-licensed builders brand their parts as such.
If I build a new VIP or something with a 3+3 Warmoth headstock, I'm putting one of those metallic Warmoth logos down the middle like on a PRS, and if I build a Mustang or Tele it's getting a Fender decal.