This is actually no different to the age old argument in hi-fi circles about whether cd transports sound the same i.e does "bits in " equal "bits out" in the digital domain,, and if not, why not. It has long been accepted that not all cd /digital transports sound the same, i.e. 'bits in," does not necessarily equal "bits out", indeed, transports have been engineered to sound different, but still people continue to argue that as nothing is apparently added or subtracted, the output of a digital transport must be the same as the data on the disk. Whatever the reason for this, and there could be many e.g. political posturing; lack of transparency in the system to notice the difference, a lack of willingness to actually, a lack of exposure to high quality audio equipment to be able to notice a difference (i.e. not knowing what t listen for) or a genuine lack of being able to hear a difference, which does not mean the difference doesn't exist.
Jitter has long been discussed as one of the reasons why digital transports sound difference, not that there has really been any consensus of what the term really means! Within audio circles, jitter refers to the timing of the digital data stream of ones and zeros - problems arise owing to the need for the said stream to be converted back into music with the same timing as when the content of the disk is first digitised. Failure to do so leads to timing errors in the PS range, otherwise known as jitter. As I said, digital transports can be designed to sound different, and much of this effect is achieved by focusing manufactured jitter on particular spectral frequencies of the S/PDIF signal – easy to pick up though an oscilloscope, and more commonly through the sound of the equipment.
Not all jitter is a consequence of the S/PDIF signal – much is a consequence of the digital processor's word clock i.e. The point at which the DAC converts the digital signal into an analogue output. Timing errors s in the clock produce voltage errors in the DAC's analogue output signal, degrading performance. The reclocking by the input receiver of the incoming clock from the S/PDIF data stream establishes the timing reference for the processor, hence not all signals to the said processor will be 'equal' across different digital transports. The level, and therefore impact upon sound quality of word-clock jitter is a consequence of many variables and interactions, including the level of jitter from the transport, residual RF hash from the transport (very common problem with PC components but some of which can be eliminated by low pass filtering) S/PDIF interface, the degree of filtering, the DAC's intrinsic jitter etc etc - whilst some transport jitter is filtered by the input receiver's PLL, anything above the jitter attenuation cutoff frequency (normally around 25 KHZ) is passed, degrading / changing the sound quality.
In the world of electrical engineering, there is no doubt whatsoever, that not all digital transports sound the same, but any notion that jitter only has a detrimental effect on sound quality haste be treated with some caution – as this may actual result in a less 'true' sound but one which the listener enjoys more. As for the Mac Mini, it is fantastic at what he does but it is not a tool designed for audio use – indeed, many of it's components are low rent even by tropical PC standards – and if you compare the internal and external build quality and sophistication of components between it and expensive audio players, it will be found baby wanting. And yes, there will be sound differences based upon it's interaction with DACS but in many cases you would need revealing and transparent (therefore costly) amplifies and speakers to notice the difference, and also, be attuned to know how the differences are manifested, which few people actually are, besides, requirements differ in all things in life, what is good enough for one person may not be for someone else but that doesn't mean each has to dismiss the other's point of view. All electronics products are a series of compromises, a PC tends to have more than audio-alone products when used as a hi-fi, so, no, a £700 PC can not compete with a £8000 CD transport but it was never intended to. As for my personal usage, I use a USB DAC into my Mac Mini and I feel this is the way forward in the future to address some of the challenges - but certainly not all - I have discussed but USB has a long way to go yet!