When 2 or more triggers have the same shortcut, there's a small pop up that shows the list of triggers, next to the mouse, that we can then pick which one to run.
I noticed that they are not ordered the same way they are inside the triggers' window, which I think they should, especially when they are organized a certain way.
If not by default, at least we could pick it to order it or not.
Here's what I mean:
Ah that's interesting , they should be ordered. It's it always the reverse order?
Apparently, yes... 
Weird...
My version of BTT is 3.626, if that's relevant
Also, I notice that when the first action inside a keyboard shortcut trigger is reordered, it creates a duplicate trigger option when run, as if it was a duplicate shortcut when there isn't a duplicate. This happens even when you change the order and change it back. It populates the duplicate trigger popup when only one trigger exists.