It doesn't sound as if you read much of what I said.
I said that increasing the sample rate can relax the demand on the interpolation filter - perhaps to make it cheaper, but I would have thought the cost of extra bandwidth, etc. would offset that. BUT on an 'off-the-shelf' Texas Instruments (/Burr brown) CODEC running at 44.1kHz the interpolation filter is unity gain until around just shy of 20kHz.
48kHz goes even further (unity until just shy of 21.5kHz). This means that no higher sample rate can represent frequencies up to that point any better, and those above are unimportant as no-one can hear them assuming the audio equipment even lets them through.
I did notice that there was some frequency shifting going on between the sample rates where the peaks didn't seem to align that well, but this might just be due to different spectral leakage due to the differing sample rates - you get an artefact where the pitch wanders off when you change sample rate then comes back in so its hard to tell if it lines up once it stabilises by ear (and I'm not going into the lab to find out) - this is made more difficult by the fact that the oscillators (deliberately or not) arent consistent cycle to cycle anyway and the differing sample rates may alter the performance of that also. Non-integer small shifts in sample rate can be the biggest pain in the arse when trying to get cross sample rate consistency (I haven't checked, so I don't know if the virus is fixed or floating point so I couldn't begin to guess why, either, to suggest how you would rectify it).
Either way, I'm not surprised, if you go into the minutest detail, that you see a difference, because they are different, the sample times are different, the banwidth is different and, yes, tinkering with the virus at 44.1 you do notice a little less sharpness at the top end which really surprises me..
I don't know what codec they use in the Virus, but thats irrelevant to the audio you get via USB as that won't go anywhere near a codec so the interpolation filter must be implemented as an FIR or otherwise on the DSP which may explain the effect you see...
Again, all I've heard arguments for is why 48 is better than 44.1 which is perhaps a deptracated problem, mainly because 48 is pretty standard for everything besides CD now and any codec I'ved used is fine on both for human ears, even on unrealistic tests, but historically may have given you a bit more margin for error. I guess it's also associated with something to do with the virus, and not having seen a line of code for the os on the thing, is all guesswork.
I'm confused, anyway. When it comes to recording the virus, can you not just change the sample rate temporarily while you do it to 48k or 96k, whatever floats your boat, and then change back when you are done? If you are using it TI mode then it has to be consistent with sample rates, so I'm not sure what they can do for you without implementing some sort of SRC in the VC plugin beyond simply doubling up the samples, which I guess is happening somehwere along the line already for 44.1k...