I think they are over-priced. Their "Power Macs" have always been quite a bit inflated.
I'm actually a little surprised they sell many of them. I remember when I bought a Power Mac G4 back in the day. It was a great machine, but it was severely over-priced. But I bought it because of software. I was in Pro Audio at the time.
Nowadays though, the advantage of the Mac Pro is falling off a little (maybe a lot). Standard computer components alike, you can get an equal or better machine for less. A ton less if you can build it yourself. And if you're a "pro" you should be able to.
Again, yes, pros could certainly custom build their own machine if they wanted to (and many do). But it all comes at a certain risk...
Many custom PC builders source their parts from online stores (like Newegg, for example) to save a few bucks and to avoid paying sales tax. The more skilled builders will certainly spend a fair amount of time researching individual parts and the various issues some of them may have when pieced together. And for others, it may be their first time doing a custom build and they'll simply slap a bunch of parts together (perhaps based on individual reviews) and call it a day.
But in either scenario (seasoned expert or novice), the potential for something going wrong is still there, as it would be with an OEM machine. Let's say for example the machine lost video for some bizarre reason and there wasn't a (compatible) spare graphics card lying around for the user to test. So, the user calls up the manufacturer, obtains an RMA and might wait a week for the new part to arrive. Finally, the new card arrives and with much anticipation, the user slaps in the new card only to be soul-crushed because he still still has no video. Okay, now he's thinking the motherboard is the culprit and now has to the call its manufacturer for an RMA. See where I'm getting at?
The OEM customer wouldn't necessarily have to deal with this, given the same scenario. Apple offers mail-in service AND store drop-off, while many manufacturers of professional PC workstations include on-site, next business day warranties. For a lot of businesses, this is the difference between losing a day of downtime and several. Do note that I'm not necessarily saying that this would apply to YOUR business in particular, but you can't assume that every business is the same.
Build the computer you want. Same thing can be same for cars; I'm sure you can go and tune a car (oh wait, you might need to build it from scratch to make it worthwhile); instead of buying that Bugatti Veyron for $1.7M; you can tune up many cars to be faster and more agile than that Veryon for a tenth the price (if not even less), but does that make it the same thing? No.
Agreed. I can make my GTI every bit as fast and agile as the Audi S3 using upgraded components (bigger turbo and intercooler, upgraded exhaust, upgraded fuel pump, bigger brakes, suspension, etc.) and save at least $20k. But would I want to risk the increased likelihood of things going wrong versus buying a real S3 (whose parts are covered in the bumper-to-bumper warranty)? No. And it would still be the same old GTI, only enhanced. And on a side note, it's resale value would be poo, because most wouldn't consider buying a used vehicle with a aggressive, out-of-spec mods that may require significantly more maintenance.
In the end, I think that really, this comes down a difference in philosophy. Neither way of thinking is necessarily wrong.