Tagging @peternlewis because I'm not sure if I'm missing something here...
I am not able to get the new %PromptWithListModifiers% to act on the ⌃ modifier. I've tested it with the ⇧, ⌥, and ⌘ modifiers and it works, but when I try and use ⌃ modifier nothing happens.
I've attached a screen recording as well as the test macro I'm using so you can see the issue. Perhaps I'm doing something wrong?
EDIT: I tested a few combination modifiers and got unexpected results when using the return key (but no problems when using the mouse). One combination launched something via Alfred, and another caused the macro to error. Did you try ⌃ while using the mouse to make your selection from the prompt? It may be you have keyboard shortcut conflict.
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FWIW all the modifiers seem to work for me, including ⌃:
Curious, are you just testing the new token, or do you have a use case in mind?
Hmmm... it turns out it was conflicting with a Typinator shortcut. I'll have to change it so I can use this new feature.
I do have a use case in mind. I have a macro to tag all files I have selected in Finder, and with this option I can easily have it add, remove or toggle said tags depending on which modifiers are down. Granted, I was able to achieve this before by placing an If action after the list, and then setting variables according to which modifier key(s) were down, but this is cleaner.
I'll have to change it so I can use this new feature. 
