Hello!
I have the plugin window and the options window (juce::DocumentWindow) in front of the plugin’s window.
At Ardour, when I show the document window, the plugin window becomes non-visible (yes, I tried set always on top for the main window).
At Reaper all OK.
I understand that it is a host issue, but is there some way to deal with that?
I would strongly advise against opening secondary windows of any kind in an audio plugin. Instead, for non-modal behaviour, consider adding a ‘drawer’-style side-panel. For modal windows, use a component overlay on your main editor, along with enterModalState().
Side panel is good, but not for my design 
I have a stack with instrument slots, with FX button for each, and that FX calls a window with effects for the slot. There are simple no place for a drawer.