By honoring font choices, do you mean the ability to overwrite emojis as well? I’ve never had issues using custom/nerd fonts, but it’s true that the emojis have stayed true to the Apple style so far.
Indeed. Emoji are just characters, rendered via some font just like any text character. On non-Apple operating systems, you can select emoji sets via font configuration.
You can do it on macOS as well, but you have to disable SIP and modify/replace the files for the Apple Color Emoji font, because some widely used GUI libs are hardcoded to use it.
Idr the situation on Windows except that emoji glyphs are inherited from your other font choices, if your chosen font includes emoji. But on Linux it's generally easy to configure certain font substitutions only for some groups of characters, like emoji.
