It really does depend on which model of Fender you're talking about - there are several levels of 'USA" Fender - and how you spec out the Warmoth. Also, of course, how you put the Warmoth build together. You can order the moste expensive parts possible, but if you hack them together, drill things incorrectly and set the guitar up poorly then it's not going to be a good guitar.
For what it's worth, as someone who owns and deals with American Fenders - both new and vintage - on a daily basis, and who owns guitars made entirely from Warmoth parts and also parts from other companies, I would actually say Warmoth is the least comparable with Fender, out of all the parts companies. Warmoth parts feel much closer to Carvin or ESP guitars. In fact measuring them, the Standard Thin profile Warmoth uses for necks is virtually identical to the ESP Thin U neck, not at all like the Medium C that Fender uses. The fretboards aren't rolled and the fret ends are cut at a steeper angle too, and the bodies are actually a very slightly different shape, apart from the 'Vintage' Strat and Tele bodies Warmoth now offers.
If we assume you're talking about comparing them to the standards of a Fender American Standard guitar, I would say a Warmoth can be as good as one, in terms of raw quality, but it banks on you putting it together properly, of course. The spec will still be different because Warmoth parts don't actually match Fender parts exactly - they're all a bit 'hot rodded'. I would say that Musikraft are a closer match if you were trying to actually replicate a Fender American Standard.
I think it's worth saying though that if the Fenders you're thinking of are more along the lines of an American Deluxe, a Custom Shop model or an actual 50s or 60s Fender, then no, Warmoth (nor any other parts company) is going to compare. Fender don't license companies that put out a product that competes with their own absolute top guitars.
A parts guitar can still be ''better'' than those Fenders in the sense that you can have it made exactly as you want it, which counts for more than plain quality, but from an objective point of view it will always be inferior. It's not a slight on Warmoth or any other company, it's just a fact that a parts guitar that costs £700 to put together isn't going to match a £5,000 handmade masterpiece.
To use myself as an example, when I wanted a basic SSS Stratocaster I bought a Fender. When I wanted a Telecaster that felt like normal Fender with the exception of all-rosewood neck and my own paint job, I used Musikraft. When I wanted a hard rock 24.75" scale Jazzmaster and a Thinline Telecaster that could do grunge, I used Warmoth.
So, have a think about what sort of spec you really want. If what you feel you really want is a regular Fender design then I think you're better off buying a Fender, using Musikraft or USACG parts or making a true partscaster out of second hand Fender parts from eBay. If you want something that feels more modern and custom, go with Warmoth. They'll all result in the same quality, it just becomes a question of the sort of feel and tone you're after.
