Just sharing a solution as it was a bit counter-intuitive…
(Using Linux with MATE desktop and Marco window manager.)
Problem
Plugin window was staying in front of the window from which it was opened (editor or mixer), but not the other. For instance, if opened from the editor mixer, stays in front of editor, but falls behind mixer window (when mixer window in foreground).
Solution
Preferences > Quirks > tick ‘Float detached monitor-section window’
This is the only ‘Quirk’ option that fixed it, so plugin window stays in front of both editor and mixer. Not immediately obvious as it mentions only the monitor section.
Background
Why the problem arose may also be useful: I was getting ergonomically frustrated with the plugin window opening far away from where I’d double-clicked to open it (and potentially disappearing behind the other window). If I double-clicked the plugin in the mixer channel strip, it might sometimes open in front of the editor, adding mouse movement.
I think the ‘first run’ plugin window opens close to where it’s double-clicked (ergonomically ideal), and thereafter remembers its own position: if I originally open it from the mixer channel, it’ll appear there, nicely. If I later open it from the editor mixer, it’ll still appear over on the mixer window. Confused me for ages, before I realised the plugin window was remembering its previous position, not where I’d just opened it from. I probably further complicated matters by working on the project from both laptop and dual-screen desktop, so the ‘remembered’ window position was probably based on the setup I’d last opened it on.