Just some thoughts on the behaviour of the menubar icon.
When I add something like a note or a screenshot the window stays put. Normally I would add a screenshot or a text note and expect it to go away once I have added it to the database.
It goes away if you click off the screen.
Perhaps you could change the default behaviour that if you have added an item, the window disapears.
Whether the Sorter auto closing after an action is dependant on how the sorter was opened. If it is opened by clicking the icon in the menu bar it will stay open to until it is dismissed. This is to allow multiple records to be added without reopening the Sorter.
If the Sorter is opened via dragging a file or a hotkey it will auto close after adding a record.