How can I make sure that Firefox doesn't use my GTK theme in the non-chrome part?

You can specify a light GTK theme to use for rendering webpages in about:config. This is great because your system theme will still apply for menus, etc., but the webpages will be rendered as they are with light themes.

1. Navigate to about:config in your Firefox browser
2. Right click and select "New"→"String"
3. Enter widget.content.gtk-theme-override as the name
4. Enter a light GTK theme that you have installed on your system for the value. e.g., "Arc"
5. Restart Firefox

Source: https://www.reddit.com/r/firefox/comments/6rbvvw/photon_rectangular_tabs_have_landed_in_nightly/dl4318f/

See also https://bugzilla.mozilla.org/show_bug.cgi?id=1283086