When hekili is disabled, I'm able to edit my elvui settings just fine. However when Hekili is enabled, the options buttons are covered up by a box that doesn't allow me to click on anything behind it.

You can view this here:

Hekili enabled: https://i.imgur.com/jD3lCqm.png
Hekili disabled: https://i.imgur.com/DHMzAZc.png

Had a look through the hekili settings and nothing stood out to me.

update your elvui to 12.17 then its fixed