My experiments with scratch builds using Warmoth components have been pretty successful. I've done four: a J-bass, a P-bass, a Strat and a Tele. The basses turned out to be among the best I have ever played. This one came under a grand:
I got all the parts except the bridge and straplock buttons from Warmoth. The neck (wenge/wenge) and body (ash, Seafoam Green---not as blue as it looks in this picture) were from the showcase---I didn't custom order them, but at current prices I think I could still bring this in under $1K. (Pickups are DiMarzio Ultra Jazz; bridge is a vintage-style Fender bridge.) (Not sure why this picture is upside down, but oh well.)
This one was built on a Sage Green Fender body with a Warmoth J-width neck. Again, one of my favorite basses ever.
The J-bass above was simply not available if I didn't build it myself: as far as I'm aware, nobody makes a production J-bass with a wenge neck. The rest of it's not that exotic, but for the convenience of getting a new body finished in a color I liked right away, I don't think I overpaid at all. Even if you don't focus on the specific characteristics, I am skeptical that I could have found a better playing and sounding J-bass of similar quality for much less. Regarding the second bass, some companies make P-basses with J necks, but again, it's not common and especially not common in green, which was a key factor in that bass. I probably could have gotten a cheaper neck---I got that one out of the showcase and to get the features I wanted I paid a little extra because the one that was available was more figured wood than standard. But I liked how it looked, and I didn't want to wait while they custom-built one for me.
After I had bought these necks, I built a bass for a friend that used a Mighty Mite neck, and it was really quite nice, for a lot less than Warmoth would charge. Depending on what I was doing, I would certainly consider that. But they, and USACG, for all their virtues, are basically in the "we do both kinds of necks: maple/maple AND maple/rosewood!" school of production. If you want something different, they are not really options.
So, I think that my Warmoth bass builds were definitely worth what I put into them, even if I might have been able to reach approximately the same place for less money with the P-bass, because I am really very happy with how they turned out. I don't know that I would go to the effort, expense, and time expenditure necessary to build a bass if it was a configuration that was readily available. For instance, if I was really jonesing for a black alder-bodied P with a maple/rosewood neck, I'd just buy a Fender. But to get something with an atypical configuration or from more exotic wood, Warmoth is a good option.