Hammerspoon is doing the stuff talked about here using event taps. I don't know if you can reliably use event taps to simulate different modifiers though, or to prevent a modifier from actually taking effect (e.g. if you wanted to remap one modifier to another).

I'm hoping Karabiner Elements figures out some solution going forward. It still works on Catalina but the expectation is the "legacy kext" will no longer function on 10.16.