A suggestion, as I've been looking for a way to get a specific behavior I want.
A 'default filter' option that lets you input a string. If you have the clear filters option selected and something entered here it sets this as the filter instead of clearing it, and if you have nothing set here it works as it does now.
Using this option would allow the hotkey by default to call a shuttle only to designated shuttle stations while still being able to call a shuttle to an arbitrary station by using the hotkey with the station's UI open, and setting the option up as described above should keep things working as they are now for those who don't want or need this.

EDIT: I think I got it working, but haven't tested it extensively. https://drive.google.com/open?id=1oLDTMfUtMcQRUiVn6spWiH-EOR3CU5TI