I am on MacOS. I can't help you in regards to the linked profile directory, if you think it needs to be set that way I believe you. But, I did set up userChrome.css the other day and I couldn't get it to work until I went to about:config and toggled the following to True:
toolkit.legacyUserProfileCustomizations.stylesheets
layers.acceleration.force-enabled
gfx.webrender.all
gfx.webrender.enabled
layout.css.backdrop-filter.enabled
svg.context-properties.content.enabled
Now this is specifically what I did for a userChrome.css not .js but most guides I found only said to toggle toolkit.legacyUserProfileCustomizations.stylesheets
but it only worked with those additional flags set to True as well. Maybe this will help you out some.