Is it really that the HDMI PCM audio protocol is flawed or rather the receiver implementation in some AVRs?
It is lossless data after all, and if there is a way to either transmit the clock or a buffer on the receiving side and a handshake so that the receiver can ask for a resend if it cannot keep up, I don't see why HDMI per se should be flawed.
The things Amir has measured seem to be due to poor analog design and/or signal processing after the data have been recovered from HDMI.
Also, there are a lot of audiophiles out there who use a PC or Raspberry to implement crossover and room correction and some old AVR to play it. I have not heard any complaints about dismal audio performance from that corner yet.
Amir did a review and measure of HDMI vs other digital input a while back on this forum. Give that a read to see the impact. It's really disappointing. Then try an experiment yourself with your HDMI AVR. Play your music source and track of choice through HDMI input. Then unplug the HDMI cable and play the same source and same track through toslink or Ethernet input depending on what your AVR supports and listen to hear the difference. If it is all the same to you then you don't need to worry. If it sounds like someone through a blanket over your speakers and all the life and dynamics was sucked out of the music then you heard the impact of the HDMI noise.
I did this with my Firetv using tidal, Plex, and Spotify vs sending the same music directly to my Denon x3100w via Ethernet and the difference was night and day audible to everyone in the room.