I've got 3 and the parts for a fourth. I think they are worth it under certain circumstances. My 3 main ones were built between 2003 and 2007, and frankly, I don't think Fender quality was all that great at the time, or, more correctly, they just weren't making instruments that I really cared for much. Interestingly, some of the spec changes I made to mine (hotter bridge pickup on my strat for example) ended up being incorporated into later fenders. For all three, I paid around a thousand bucks for parts and assembly. I did some of the work myself, which saved some, but I have a feeling the guy who did the final set up/nut etc also probably had to fix some of my wiring. A well assembled Warmoth, in my opinion, meets or exceeds the quality of Fender's non-CS stuff. Big downside is that they take a massive hit on the resale side.
Strat- This was my first. I wanted a hardtail (in retrospect, maybe I didn't, but at the time I did

) which I don't think fender was making at the time, I wanted better pickups than what was in the American Standards at the time (went with Rio Grande), I wanted an ebony board (never an option except CS), and I wanted better color choices than fender was offering at the time in my price range (I went with LPB). Overall, I'm pretty happy with this one. Sounds great, plays great. Only regret, in the end, was the hard tail, which I think pushes the tone a little in the tele direction, which would be fine, except I also own a tele. I think, with case and assembly, came out about 150 bucks cheaper than an American standard was going for at the time, and I think it was a substantially better instrument.
Tele- Liked the strat so much, also did a tele. In retrospect, I probably should have just bought a fender, as this one is more or less 52 reissue. Came in a little cheaper than a 52 RI, and that includes a fancy pants Callaham 3 barrel bridge with compensated saddles. Two negatives- I went with a 1 5/8 inch neck, and that turns out to be a bit narrow for my taste on a guitar (yet a bit wide on a bass, I'm picky). Also, I paid extra for a birdseye neck, and there just isn't enough birdseye on it to justify the upcharge.
J bass- This has become my main work horse instrument. I played about 50 Js (I'm not exaggerating) and just couldn't find one I liked apart from vintage stuff that was way out of my range. Alder Body, maple/pau ferro neck, stainless frets, Nitro finish (matching headstock, oly white, sprayed by a relative). Norstrand NJSV pickups (humcancelling J, vintage voiced), audere preamp. This thing is just killer. I get all kinds of compliments on the sound. Price, including case was comparable to an American standard at the time, substantially cheaper than their active American made basses at the time.
P with a J neck. This has been sitting in parts in my basement for a year, probably need to get to it. Fender doesn't offer a ton in the way of P's with J necks. I had MJT do a matching headstock charcoal frost Nitro finish, and some aged hardware. Novak pickup. Probably will end up costing more than a fender would, largely due to the finishing price (which was totally reasonable, but not free).
Edit
I also briefly had a fretless mongrel from ebay (had totally forgotten). I was looking for a beater to learn to paint on (never did paint it), got the carcass of a J bass for like 100 bucks, shows up and it is a warmoth neck and body. Sold off the neck and parts, bought a new warmoth fretless neck. I ended up selling it because the body was solid maple, and the whole thing must have weighed 13lbs. And also, because I found a good deal on a carvin 6 string fretless. Never did repaint the poor thing
OK, if that was too long, here are some questions to ask yourself
1. Do I really know what I want?
2. Is what I want meaningfully different from something I can buy off the shelf from somebody? If not, just buy the stock model.
3. Do I understand how the various things come together to make a bass (wood, pickups, neck dimensions, etc).
4. How much am I willing to take a gamble? Unlike an off the shelf instrument, you don't get to play it first. I've been really happy with my 3, but it is pretty nerve wracking to get all the parts, do the work, and only then find out if it sounds good or not.
One other piece of advice- Consider buying off the in stock page. You save a little money (though I think they used to have better deals) but more importantly, on bodies, you know what the weight is (they don't weigh necks for some reason), and on both, you know the grain. I'm not super picky on weight BUT I have seen alder J bodies north of 6lbs on there, some pushing 7, and you could end up with one of those if you order from scratch. Also, unless you do the "
unique choice" top selection for figured wood, you just get luck of the draw, and some of the figured maple tops I've seen are pretty lackluster (but the unique choice is another 100-250 upcharge)