You're right Clueless. It is very site dependent. First, mods are performed with the intent of increasing the enjoyment (read performance) from a particular piece of equipment. Rarely is thought given to "resale" because the hope is that the improvement will allow the component to stay in the system longer before a complete change is desired.
True, the cost of the mod parts and labor are rarely recouped, but that is secondary to the desire of improved performance. Certainly, the qualifications of the individual performing the mod is worthy of consideration, but I find it rather amazing that people seem to be under the delusion that a factory mod is performed by the designer himself. Rarely is that the case.
Not to diminish any of the accomplishments of any one audio designer, but very few have created anything "new" in terms of audio design. Most have improved previously existing circuits through better components or novel approaches, and improved marketing. Sorry, folks, but they're not gods.
For a retailer having to deal with customers that have no knowledge of electronics, I can understand the business decision to avoiding handling modified gear. Most of the dealers aren't EE, so they can't explain the mods or their intended improvement, and few customers have the luxury to really listen to stock versus modified equipment before purchasing. The same is true for many of the hobbyists at this site. This is unfortunate.
However, modified gear can be one of the best bargains on the used market. The buyer should expect improved (usually much more expensive) parts for which the manufacturer would have to charge 4 or 5 times the cost. Yes, manufacturers are concerned about getting a "sound" from their gear, but first and foremost they are in business to make a profit. Almost all products are designed to a price point, so the cost and availability of individual components is very critical. Rarely is the "best possible" component used as opposed to the "best possible component at a price". To improve profitability, the cost of the components and/or labor to assemble must go down, or the retail price goes up. This usually necessitates a "new and improved" model to justify the price increase, and the circle begins again.
There is an advantage for the industry to keep audio rather mysterious so that we must all worship at the alter of our favorite designer/manufacturer. For those who wish to follow, I hope you have the money to support the mark up (x4 or x5) for the "mods" (again, mods at a price point) that your favorite designer has incorporated into his/her latest new product which you will likely pay big bucks to acquire.
I'm sorry if I've offended anyone with my diatribe, but audio mods can be very worthwhile for all current and future owners of the gear. Get all the info you can on the mods and the qualifications/background of the installer. Then, if you determine that the mods were of quality and of value, go for it. You just may have purchased the next generation (or beyond) of your favorite manufacturer at a fraction of the cost of that "totally new" model which by the way, just went up in price by 20%.
Enjoy the music.