The issue on their public issue tracker has been open for something like 8 years.
Unfortunately for me this means that no keyboard shortcuts using the Cmd key work, despite me using a built-in macOS keyboard layout with no special customisation.
I also use a built-in macOS keyboard layout with no special customisation, and I regularly use shortcuts with Cmd. Perhaps you might want to change your Keymap in IntelliJ(this can be done by Double Shift -> Type Keymap -> Select new value.
Edit: For me, almost all the shortcuts detailed in this post work, just need to replace Ctrl with Cmd.
This can get a little confusing, but most common shortcuts contain the Cmd modifier on a Mac, so it's only really Terminal/iTerm where things are different.
My keyboard is still physically a QWERTY keyboard which makes knowing where Cmd shortcuts are very easy, I can just look. I switched to Dvorak when I was 18, but learnt with a Dvorak keyboard so I didn't learn it well enough and when I got to uni and had to use shared lab machines I couldn't manage and had to switch back. Then just over 3 years ago I had 3 weeks off work so switched at the beginning with no physically different keyboards and learnt it all by position and I'm still using it today. Less hand pain, and I can touch type where before I was proficient but not entirely by touch.