Yes I think noise is the issue even though the signal is reclocked and resampled by the DAC.
The BDP-3 Digital player is really an optimized computer for digital music playback including all the things you mentioned like proper power supply and circuit layout to reduce noise etc. The thing with generic computers is we have found there are a lot of processes going on in the background that you are just not aware of that can affect performance - Widows KMIXER is an example.
I would say though that an educated computer person could certainly setup their MAC or Windows computer to emulate what the BDP-3 does. I see the BDP-3 as a way for our customers not to have to bother with the complexities of normal computers.
That's a very honest reply!
However, I must be honest too and say I spent a lot of money getting my PC to a point where I'd be satisfied with it performing as a dedicated music platform. This was prior to buying a BDP-1. After buying the BDP-1 and listening to it for a few months I went back to the computer and realized music coming from the BDP-1 sounded less strained. In essence, I realized all the money I spent on that PC was in vain.
Sadly, even if you buy a specialized power supply with passive cooling, specialzed cooling system for the CPU that makes no noise, select all the hardware components for minmial electromagnetic interference and have all the software installed by a certified Microsoft professional (fortunately, a friend on mine did all the software work), it will still not sound as good. You might get 90% of the BDP-1/2 performance but you won't really get all the way there.
In the end, it depends on how much you're willing to spend. Advantages of a PC are expandability even though you're still have to deal with software and potential problems with it not performing it's best and there could be a thousand reasons for that. Every time Microsof issues an update, it is automatically installed onto the system and this usually causes some problem. Not always, but it does happen frequently.
BDP-1/2 don't suffer from these problems but it does cost more. I now own a BDP-2 even though there were really zero improvements over the BDP-1 in terms of audio quality. The reasons for upgrading were rather pragmatic and again - software related. The BDP-1 just couldn't handle my home network without interrupting the playback.
As always, it's horses for courses.