I tried this with Totem and Ristretto: If "Automatically show and hide the panel" is set, the hidden panel is visible as a small line at the edge of the screen even in fullscreen applications. (The non-hidden panel is completely invisible in fullscreen mode, as expected.)
Created attachment 3580 Fix it with GTK_WINDOW_TOPLEVEL This patch, which makes the hidden panel a GTK_WINDOW_TOPLEVEL with "keep above", fixes the problem for me and so far does not seem to have any undesirable side-effects.
Applied in 27dfa9b.