Yeah, I just figured the safest option would be to only set the actual document root element transparent - in practice I think it's possibly more likely that the `` element has background set by the page - although the page might as well set both. So yes, it depends on the website.
I don't think I understand exactly what parts you want to make transparent, but this does work:
browser.tabs.allow_transparent_browser
totrue
#main-window, #tabbrowser-tabpanels{ background: transparent !important; }
html:root{ background-color: transparent !important; }
The above would make window background, and the are behind web-content transparent as well as background of html documents - otherwise the background of browser area wouldn't show up anyway. Toolbars that have their own specified colors would still be colored - which might be opaque or not depending what theme you have selected.