I don't want to be biased and I think you bring a lot of important points.
They're not bad for your setup, they're bad for people who want to create new stuff using today's technology.If the HC chips are bad for my setup I haven't noticed it and hopefully wont.
Normal TTL-LS have a threshold voltage of about 1.5 volts while HC chips running at 5V have this threshold at about 2.5V. Whatever is below this voltage is a zero, whatever is above is a logic 1.
TTL-LS chip usually signal a zero between 0.3 and 0.7 volts so that's no problem and they signal a 1 between 3.4 volts and 4.2 volts so it's not a problem most of the time.
However, cartridges like Easyflash 3 and 1541 Ultimate 2 use low voltage CMOS chips which signal a zero at about 0.1-0.2 volts so that's no problem but they can signal a 1 between 2.6 volts and 3.3 volts and that can become a very big deal.
If newer stuff comes along that uses 2.5 volts CMOS then it will work well on all normal C64 but not on the C64r because half a dozen chips on it should have been HCT. HC and HCT chips are exactly the same price...
You also saw the "couldn't be bothered" attitude of Jim Drew and Schönfeld.
I was actually very interested in buying a C64r until I noticed this problem. I got completely turned off when I saw Jen's reaction.