I haven't looked at new Fender basses in a long time but I do know Tele models, so here's an example: Choosing the modern Tele and outfitting it just like an American Standard gives me a price of $1500, but you can buy the Am Standard for $1250 MAP, and if you know where to shop, you can get it for $1100. So why would you want to go this route? If you wanted any of the three other pickup options, you'd still be much better off buying an Am Standard and then buying the pickups separately. If you wanted the Am Deluxe neck ($200 upcharge) you'd be better off just buying an Am Deluxe to begin with.
If there were more custom options -- say, being able to choose fret size or different pickup configurations -- then the extra cost would be justified. All you're getting now is different off-the-shelf options, and the extra cost just wouldn't make sense for most buyers.
