I don't know, IMO it would be better solved by profiles, environment specific settings (eg. settings.json + settings.windows.json), or override keys, eg:

    {
      "font": "xxx",
      "[windows]": { // windows overrides
        "font": xxx
      }
    }

I know using a full fledged programming language is infinitely more flexible, but I'm not sure a config needing infinite flexibility is a sign of good design.

If they want to stick with Lua I think they should allow both: write your config in JSON for the 99% of config that is easy, and allow to modify and return an updated config in Lua. TBH I just downloaded Wezterm a few minutes ago and got bored just wanting to add a Cmd+K shortcut to clear the buffer.