Ukele seems to be about character output, and doesn't interfere with the actual physical key behaviors or modifiers (that's what I get from the site and the interface when running it).

For instance I need the Left and Right Command keys to each switch on/off the IME when single pressed, and act as Command when combined with other keys. Same way the Fn key doesn't seem to be mappable.

Seems to work at the same level as the Powertoys remapper on windows, minus the shortcuts.