Karabiner works by fetching the input key with its “flags”. So the key code a is different from ⌘+a as an input and so on… keep that in mind when combining mods.
When you have, let’s say, caps lock mapped to output ⌃, then you need to hit caps lock key before hitting any other modifiers. Else, it will trigger caps lock, since ⇧ + caps lock wasn’t mapped to ⌃ + ⇧.
Now I’ve made the jump to the bizarre land of custom mechanical keyboards and use a ZMK Ferris Sweep (if curious, here’s a pic). So every bizarre mapping now lives into the keyboard. But I was very fond of Karabiner before and definitely will use it should I not bring my Sweep with me elsewhere.