The CPUs, GPUs, hard drives, RAM, etc are all available for PCs as well. The logic board is custom, so is PSU but you can get equivalent for PC (with similar ports, wattage jadajada). Older iMacs like mine uses a custom CPU but it isn't that special, just a model between mobility and desktop chip so the only difference is the TDP. I can walk in store and build a similar machine to Mac Pro, with pretty much the same parts.
CPUs can be swapped if they are suitable for Mac Pro. You can also flash certain PC GPUs to work in Mac Pro.
As far as I know, you can put normal CPU to single-CPU Mac Pro but the UP version (the same chip as normal but with ECC support) costs the same anyway. In dual-CPU MP that's not possible as non-Xeons have single QPI and thus do not support multiple CPU configurations. You can also use non-ECC memory I think but then ECC will be disabled. The heatsinks are pretty specific though.
Those are the only custom parts in Mac Pro, others are pretty normal (the GPU is the same you can buy for PC but has some custom EFI and drivers etc)
CPUs, GPUs, RAM, HDs.... All are parts I can get from the nearest computer store.
Last time was yesterday when I was at work, building a PC. Apple doesn't use any higher grade parts than PCs. Of course 400$ Acer will have worse parts than 2000$ Mac Pro but if you get a custom PC, you get even better quality, let alone warranty. The thermal paste Apple uses is the cheapest crap available, people who have reapplied that have gotten like 20c temperature drops. The quality in PCs varies a lot, you can't say all of them have bad cooling and wiring.
Again, compared to what? Yes, the 400$ Acer might have worse stuff but if you compare a PC with similar price tag as Mac has, you are getting good quality, especially if you build one on your own.
Much easier to fix something on a PC as you can use any part that is compatible. If you mobo fails, you can grab a new one from the nearest store for 100$. If Mac Pro's mobo fails, you have to hunt one from eBay and pay ~400$. Most PC components come with 3-5 year warranty, Mac Pro comes with 1-year, that's already one great benefit.
They share almost everything but the design. What would have to be the same so you would think they are the same? They use the same technology, equivalent parts thus they are the same. The software is the biggest difference between them.
The stuff inside Macs are what you can find from PCs, nothing special. They aren't any higher quality, infact, you have a lot more options when choosing a PC i.e. not limited to one logic board with limited ports, you can jump for an EVGA board with 7 PCIe slots. As I said, the quality varies. Macs are above the normal quality of OEM PCs IMO but still not the ultimate high-end.
I prefer Macs but in the end, they are just PCs with fancy case and OS