Yes, on wayland you will need to run a particular program as root to be able to read all keyboard input. See xremap or mouseless (unmaintained).
Since you already give the program plenty of trust to let it read all your inputs, I think running it as root is not outrages.
That being said, in an ideal scenario, we would be able to set fine-grained permissions like, allow to read keyboard input but deny communication with other app, networks, and storage etc. But I don’t know any OS that can do this.
A more straightforward way to remap key is to get a keyboard with QMK firmware, that doesn’t cover all the use case of ahk, xremap, or mouseless, but that don’t require you to trust another program to run as root.