I suggest moving Console's commando toolbar to the toolbar in Console's dockable window rather than place it on jEdit's toolbar. I always hide the jEdit toolbar so I have more vertical space for the text area. I suspect most people dock Console at the bottom, so there is plenty of room for a toolbar. Another option would be to put the commando items in a dropdown to select rather than individual buttons on a toolbar.
I hate the toolbar, I always have it hidden.