I can see both sides of this debate. It reminds me of an exchange a few years ago on AC between a prominent AC manufacturer and a prominent AC modder. The modder wished to modify a pair of the manufacturer's amps, and contacted the manufacturer for some reason (perhaps simply to ask for his blessing). The manufacturer made it clear that he disapproved of the effort, and threw down a challenge. The manufacturer claimed that changing the value of a single resistor or capacitor or some such thing would improve the performance of the amps significantly, and asked the modder if he could suggest which component could be changed. The modder declined to rise to this challenge, and consequently the manufacturer dismissed the modder's efforts as misguided.
I think this sort of experience supports Roger's claim that modders often? at times? occasionally? don't really know what they are doing. But it doesn't mean that the modder has nothing of value to offer. In the case of the particular modder involved above, we're talking about a guy who has modified things for MANY of the people who have visited AC over the years (including myself). His work has met with overwhelming levels of satisfaction. He seems to be a thorough experimenter, rather than a designer like Roger; but many believe that his efforts make real and significant improvements in the performance of their gear. Moreover, his reputation for taking care of his customers is fabulous. In my several dealings with him (only some of which were regarding modifications) he's really established himself as someone who wants to leave his customers satisfied.
Undoubtedly, there are less scrupulous modders out there - and in the event that someone sends something to Roger to fix, it's obviously a case where the modder has (a) not produced something to the liking of the customer; and (b) failed to stand behind the product adequately. But these characteristics are ones that are potentially exhibited by designers and producers of NEW products as well. There are certainly modders I would never get to work on my gear (certain advertisers on Audiogon spring to mind, whose modifications always seem to have exactly the same effects on the huge range of gear they modify, and always involve the flavor of the month boutique parts). But there are also manufacturers I would never deal with because I don't get the impression they know what they're doing, either.
The thing I take from all of this is that reputation is valuable. Music Reference has a reputation for producing gear with high quality sound and high quality engineering, and for many that's worth paying for. You can save a few dollars, and try to get the same quality from a modder, but it's like buying a lottery ticket: you might get lucky, and you might not. The more information you can get to convince you that the modder stands behind his work, the better a risk the modifications become. But once the reputation is established, those modifications will also start to attract higher prices.
Chad