If it were possible to keep the "Properties/Options" windows (those that prevent interaction with the rest of the program until an option is accepted or rejected) on top of everything else... that would be perfect.
These types of forms should always appear in the foreground, above everything else, precisely because they prevent interaction with the rest of the program until a decision is made. If they are buried behind a plugin window, the plugin won't be able to close either.
On: Options, Tools, and Plugins Always on Top
If it were possible to keep the "Properties/Options" windows (those that prevent interaction with the rest of the program until an option is accepted or rejected) on top of everything else... that would be perfect.
These types of forms should always appear in the foreground, above everything else, precisely because they prevent interaction with the rest of the program until a decision is made. If they are buried behind a plugin window, the plugin won't be able to close either.