it's impossible to add custom XkbOptions without also adding them to the default rules.
This causes trouble since those files are owned by the distribution's package manager and thus overridden on update (and furthermore require root permissions to modify).

Expectation:  similar to ~/.Xmodmap, there should be a way to have a user add custom symbol snippets to remap function keys or similar on a per user-basis.

gnome ignores .Xmodmap/renders it useless with multiple layouts (you can run it manually, but it only applies to primary layout, not to other layouts you switch to), however it supports specifying xkboptions. But to add them you need to provide them system wide.