I don't believe MQA is manna from heaven, or the answer to audiophile dreams. More likely it's a way for the record industry to have tighter controls over the release of hi res music, while still holding on to the originals. Fine.
But the attempts at "proof" showing it to be inferior are poorly constructed and would be torn apart in any other area, if it wasn't for the fact that everyone loves to hate MQA.
In reverse order
Did any new format have to prove how it worked to the general public, maybe I missed that. People still pay a premium for DSD files, which are proven (its a fact) to be upsampled from the DXD (PCM) masters and we don't read about how its a scam every few weeks. I couldn't say what the motivation for restricting digital out is, but one could easily record the analogue out with an ADC and compare to a known like for like source such as 2L. Plenty of folk with such devices around, yet I've not seen this done?
This is a misdirection at best, someone at Warner ok'd having Neil's music converted to MQA without his knowledge. The files were 44.1khz MQA (which I agree seems rather pointless, as why bother. I suspect its due to blanket licence agreements between Warner/Tidal). There's plain old MQA and there is MQA Studio masters, these were plain old MQA. I agree Tidal's choice, to use the label 'Master' can be misleading, I'm going to give them the benefit of the doubt that they mean "the best copy they have" rather then the actual "recording master"
I agree that paying license fees is a pain, but what are these fee's really? $99 DAC's have MQA, so it can't really be that much. MP3 incurred a license cost until a few years ago. Licensing fee's are a way for innovators to make a business. Sure it could be open source, though it would be much harder for them to survive as a business and like MP3 it may well become that way eventually.
This is conjecture. "normal" and MQA files exist, go to 2L's catalogue for freely available samples. One DAC had its MQA filter on all the time, all (or all I've seen) don't do this anymore. This is no different from you leaving your DAC in the same filter mode for all tracks. MQA attempts (if they do it right, I couldn't say) to pick the best filter for a track, and one assumes in the Mytek implementation it defaults to one if it doesn't have that information. Whether linear phase or minimum phase is really better is a whole different discussion.
As to the original "analysis" comparing the bits between a plain FLAC / MQA file makes no sense. One should really compare the analogue output, but even then this isn't conclusive. Do we care what noise is left over outside of the audible band? AFAIK the USP of MQA is not providing audible information above 20khz, but to provide the timing information of higher res content. Its meaningless to diff the bits between a file that is downsamples to 44.1 and an MQA file (folded or unfolded), of course they are going to have different bits, the bit that is important is do they actually sound different? Are there any proper controlled tests that can confirm anyone can tell them apart?
I would much prefer MQA was an open source solution, that there's wasn't a premium to use it. 99% of the software I use is open source, but there is room for the 1%, and maybe MQA fits in there.