Apologies OFOTD.
I realize there is no debate about the resampling, it's there. And if I had the kind of money tied up in high quality A/D's that you have, I'm sure I would want things going into my digital bit-buckets as accurately as possible with respect to what my A/D put out. I respect that entirely, and don't mean to belittle that.
You are right, the debate is entirely in the realm of "how much" and "does it matter"? And I really didn't want to get into that, but I feel challenged. I'm not an expert, but I have enough technical knowledge to draw my own conclusions.
My particular V3 and my particular R4 do happen to align significantly better than 99.99% every time I've checked, and I've checked a few times (a ratio of 1.0 +/- <.0001 is 99.99%, and I generally get .00001 which is an order of magnitude less). On a particular day... it *could* be that the clocks randomly align, and then accuracy would be 100%... not likely for long, but it could happen. So I consider worst case accuracy 99.99%, typical accuracy 99.999%, and hypothetical best case 100%.
Just because someone has a "bit perfect" bit bucket like an R44 doesn't mean 100% accuracy. Some digital protocols like TCP/IP have checksums and retries, etc., to make SURE the data is correct. S/PDIF does not have these, so if there is jitter or noise on the line, the hardware implementer is left to "do the best it can with what it's got" which I suspect on most consumer class boxes is less than stellar, so the result may be less than 100%. For those who use AES, AES has a CRC byte, which is a checksum to detect errors. I haven't studied AES enough to figure out if it can correct the errors, probably it can, but it's pretty clear that S/PDIF can't. If you have an R4 pro, or SD744 and run AES in, you have a much better chance of 100% than someone with S/PDIF into an R44. At any rate, there is plenty of opportunity for a "less than perfect transfer". So I consider best case accuracy 100%, but no certainty of that, and I'm not sure how much less. Now to be fair, the R4 could also suffer this same S/PDIF inaccuracy. I've seen quite a few digi dropouts on different decks which are audible, so I would predict there are many many more that I can't hear, which makes me speculate the error rate is a significant.
So we have two cases...
a) The resampling R4 which is probably 99.999% accurate, and almost surely no worse than 99.99% and hypothetically as good as 100%.
b) The "synchronizing R44" which is "probably a little less than 100% but I don't know how much".
The traditional statistical tool for determining if something is "significantly better" is a Student's t-test. I have thought about doing a test where I run a known sample (a contrived wave file from computer generated data) into my R4 and into my buddy's R44, each 25 times, then analyze the output files to come up with an accuracy factor and run it through the t-test math. You know what? I decided it's too much like work, and I never bothered. And as far as I know neither has anyone else. So no one really knows if the so called "bit perfect" boxes are any more accurate in the end or not, everyone just assumes they are.
So.... I think my previous statement "There is debate that it may be 99.99% perfect on an R4 versus 100% perfect on different deck" may be overly simplistic, but I didn't just pull it out of my ass... it has technical rationalization. And I think it's a damn shame the people who own "bit perfect" boxes belittle the hell out of other people's gear, to the point where the folks who own "non-bit perfect" boxes they feel like second class citizens and spend hundreds of dollars buying new boxes just so they don't feel like second class citizens any more. I've seen it happen and I think it's ridiculous.
So Yes, the R4 resamples.