You don't have to pass the country selection into your other system. You just use it in the flow to determine the different actions taken if the submission was US or Canada.
That's what I don't understand. You say you are filtering something with the flow; but then you say everything is going into another system. Filtering implies removing something, as in form submissions with a canada zip code need to be filtered, removed.
If you want the flow to perform separate actions based on if it is a US or Canada address, then using the country selection option with the form would work. Just use the value from the option and split the flow steps.
Or by filtering are you talking about scrubbing the zipcode text value to remove spaces or something so that it can go into the other system?