While that is obviously a detractor that I would agree with, how much it affects you will vary from person to person.
Again, just myself as an example, I've been somewhat surprised over the years how little I've actually needed a super key.
On Mac OS, my preferred keybindings was to have Command bound to both left and right Alt keys, Ctrl kept as the left Ctrl key, while the right Ctrl key was rebound to Option/Alt. Some people also like rebinding the usually-useless Caps Lock key but I am one of those weirdos who doesn't like doing that.
I've moved back to Linux over the past couple years and haven't found the need to do any rebinding to get a Super key on my keyboard at all.
Again, just myself as an example, I've been somewhat surprised over the years how little I've actually needed a super key.
On Mac OS, my preferred keybindings was to have Command bound to both left and right Alt keys, Ctrl kept as the left Ctrl key, while the right Ctrl key was rebound to Option/Alt. Some people also like rebinding the usually-useless Caps Lock key but I am one of those weirdos who doesn't like doing that.
I've moved back to Linux over the past couple years and haven't found the need to do any rebinding to get a Super key on my keyboard at all.
Your mileage may vary!