Haven't read all the pages, but my thoughts -
First, any mod takes value OUT of the instrument as well as putting it IN. Anytime you replace something, by definition it's losing whatever is getting replaced. So if you take out the stock pickups and put in a set of $150 ones, you haven't added $150, you've added 150 MINUS the value of what was there already. And whatever the cost of the stock ones, if they did the job reasonably well, the "upgrade" may be a lot more marginal than the difference in price.
Second, with used instruments generally, there's a hit to value because you don't have the return-guarantee of buying something new from a retail outlet. That discounting applies to mods as well. And you don't have the security of a quality-control inspection from a manufacturer you trust.
Thirdly, the reality when shopping is rarely a this-price-vs-that-price calculation; it's more of a binary want-it/don't-want-it decision. So, for instance, I like jazz necks. A P bass modded Duck Dunn-style with a J neck would be of interest to me. I don't much care if it was made that way at the factory or if the current owner modded it. A P bass without the neck mod is not worth less money to me; I simply wouldn't buy it at all. Fender doesn't offer this, but take, say, a G&L LB-100. One seller is selling one that had a 1 5/8" neck, switched it out at some expense for a 1 1/2" neck. Another seller has one that came from the factory with the 1 1/2" neck. The guy who modded his didn't make it any more valuable than the other. He just made it one I would consider looking at.
Or take the example of installing an Audere preamp. Sure, that cost the owner money to do. But I like passive basses. The preamp doesn't add any value at all to me; in fact, it might make me ignore that offering. It's only going to be of interest to a buyer who wants the Jazz bass BUT ALSO feels that they need Audere preamps to be desirable. That's going to be a smaller market; and lower demand means lower price.
Related to that, a buyer usually goes shopping with an idea in mind that's probably based on usual factory specs. If I want a J bass, I want a J bass, and I know what that entails. Someone may have souped up their J bass, and that's all well and good. But it's gravy on top of what I already want, at best. If I can get a J bass I like for $400 I'm not going to be terribly motivated to cough up $500 for a J bass with gravy. I already got what I wanted for the lower price. If I'm saying to myself, "What I really want is a bass with an Audere preamp," then I'm going to look at brands that have that standard, and only by coincidence might someone's used J-with-Audere pop up on my radar as I'm browsing the TB classifieds or Reverb or whatever.
