If I had to replace my Fender Strat neck (which I do, btw), I would prefer to replace it with a neck of the quality that Warmoth put out. Would I get a Warmoth neck and source a Fender decal for this guitar? For me, personally, the answer would be no.
I am however, contemplating replacing both the Fender body and neck with Warmoth parts and placing all my pickups, tuners and other hardware onto the Warmoth body and neck of my choice. While I love the sound I get from the Fender pickups and the trem it has, the neck is the wrong scale for me, and the body is scuffed up. A better quality of wood in the body and a 24.75" scale conversion neck would actually improve my opinion of the instrument.
The Strat in question is a 1983 MIJ 57 reissue, and it's resale value is low anyways. Different set of principles if I had a Custom Shop Strat or some special Limited Edition or Signature series.
If however, the neck scale wasn't an issue and the body was still OK to me, and there came a time to replace the neck, I'd be sourcing a Fender replacement neck, which I believe, can be obtained so long as you can prove the authenticity of the guitar you have. If the Fender neck got the decal scarped off somehow, I'd be miffed, but doubt I'd bother getting a replacement decal (unless it came time to sell the guitar).