Hi Kyle,
As the saying says.. : A picture is worth thousand words..
Sorry that I didn't understand what you were talking about right upfront.. the 2 captures you're showing above are actually different (1st is for Macros & 2nd is for Shortcuts).. Technically it probably both run your .mac files... but the point is that you should be very careful about using F-Keys to assign to shortcuts or macros.. I'm basically staying away from this, since there is so many system interaction that could be intercepted by an F-key assignment... just thinking about my own screen capture software that has not less than 16 'hotkeys' assignments and those could all interfere with something else in the system (like a simple CTRL-P for print box dialog)..
I know that shortcuts can be very useful for repeating tasks, and myself have a lot in my navigation pane on the left side, but none of them actually are assigned to a 'hotkey', since this can depend on the context you're running in.. Windows can sometimes be very strange.
PS: I just tested this with my Screen Capture program, and the hotkey took precedence on the GP assigned macro/shortcut... so be aware about this.