I'm looking to put together a Warmoth bass. Just finished putting together 1 Warmoth guitar for my friend, and he's already ordered another that I'll be assembling for him. I will warn you on price - you can get a used USA Fender for less, and that Fender will have the same value a year later.
There's a couple "problems" with Warmoth:
1 - The price of a standard body is around $200. The cost for them to add paint is another $200. That's $400 for a regular body, no options, nothing fancy.
2 - Their "menu" is almost endless, so it's easy to bump yourself up with an upgrade here and there and it quickly gets carried away.
There's a nice "solution" though, and that's their showcase! They have premade (and sometimes prefinished) bodies and necks for a reduced price. As long as it is what you want, you'll save a decent amount by buying from the showcase. Plus, you won't have to wait a couple months for them to build your custom body.
Even using their showcase, you'll probably spend $600+ on a body and neck. Then you have to add all your hardware, pickups and electronics. Figure another $200+ even if you go the ebay/used route. So you can see how you'll spend $800 on the bass. And yes, resale is usually poor - figure $400-500 on a regular no frills model.
That said, after my experience with Warmoth, I am definitely going forward with my bass build project through them. It will just take a bit of time to save up to buy the pieces here and there. Since this won't be a bass I intend on selling (if it comes together right), I won't worry about resale.