I don’t think the ‘always on top’ option for Plug-In editor windows makes a difference. On my system (Cubase Pro 9) the plug-in editor windows are always at front no matter if ‘always on top’ is activated or not.
This can be a problem when you’re making adjustments and then need to access the Project window for example, but you have all these plug-in windows in the way.
I’m aware one can use the ‘Close All Plug-in Windows’ key command, but the problem with closing all the windows is that if you want to go back in to edit the plugins e.g. EQs of different tracks, then you have to re-open every instance!