First I must say that AAP not only improved the workflow so much. Lot’s of recordings just sound better when it was simply not possible to get the tracks phase aligned manually.
Anyway, what would help me a lot now that I trust AAP (and my ears, if AAP did somethin wrong) would be a much smaller window. Once I selected the right Side Chain and mode I keep lots of instances open and render files with a shortcut triggering a macro. And for desktop real estate the AudioSuite window should be bigger that e.g. the Avid Invert AudioSuite Plug-In. Can you create a “minimized” version of AAP?
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This is the top requested feature after Auto-Align Post was released 
As I’ve mentioned also on other thread in that issue here.
We’ve demoed it on AES, It will be part of an upcoming maintenance update.