Where do you see, "Alternate Runes"? I look in settings Controls, and see, Alternative Glyphs. Is that what you are referring to? It looks like it has to do with a gamepad since it is under, enable gamepad.

I found this on the wiki, Alternative controller glyph style option.

It is listed under Version History, version 0.207.2, Gamepad support.

still doesn't explain what it really does though.

https://valheim.fandom.com/wiki/Version_History