For me, OEM support is one of the major disadvantages. If something fails on my home-built computer, I can troubleshoot it myself and replace the part if necessary (~30 minutes). But with apple care, I have to wait for them to fix it (takes forever)
An example: A few months ago the laser in my macbook pro superdrive failed. I have Apple Care and an Apple store 20 minutes down the road, so no problem right? Well, first I needed to make an appointment, the soonest of which was the next morning. So I go in first thing the next morning and tell them that the CD drive failed and I need a new one. They said they had the part in stock, and that they would give me a call when the repair was done. Shocked, I asked why I couldn't just wait while they do it (I've replaced these drives before in under 20 minutes) but they said they had a queue for this sort of thing. I asked if they could just give me the part and they said no. I told them I could literally do the repair right there and give them the bad drive so they could sign off on it. All I needed was the damn part, but no, I had to let them do it their way. So I go home and wait. 10 hours later, they finally call me to say that the repair is done. I lost a full day of work because of that.
Bottom line: having some company cover my repairs has always been an unnecessary hassle for me. They always need to test it to determine the problem and coverage implications, then go through specific procedure to fix it which takes forever. I don't need that. All I need is the part. That's why now I only ever use home-built machines for critical work related tasks. I know exactly what parts I used and exactly how to fix it quickly if anything goes wrong.
So yes, I think it's perfectly fair to compare a mac pro to a home-built PC since you save a ton of money AND have the added bonus of not being tied down to proprietary parts.