The main differences come down to the detail and your ability to do the job.
For example take into account the following -
The quality of the paintjob. Unless you buy a prefinished body, a home spray job will not be up to the same spec as a pro polyester or nitro job.
The fitment of the neck in the neck pocket. We've all seen necks that have been too tight in the pocket and caused cracking in the paint or the pocket itself. Of course, you can ease it in, but unless you are tooled up correctly (or have any means to refinish body/neck if you mess up) it will be hard to get that perfect joint.
Of course, it's all possible - but if you aren't already tooled up or have access to the right equipment to get the detail correct, then it will be quite costly (how many people have screening paint hanging around for example) - and remember, you home built bass with have a limited resale value. (Depends if you are one of those people who like to have a "name" (or a fake Fender decal) on your headstock... or are actually chuffed that you have something that nobody else has got...)
Having said all that, everybody should build one... it's a reqarding experience.