Thanks for your question.
There are few formal rules related to what Google will and won't do related to indexation. If Google finds any piece of information worth indexing and displaying, it will do so. Schema is a great way to tell Google what information you want displayed in search results, but it's not an explicit rule that they always follow and, in many instances, they ignore it completely.
Having said that, lots of businesses have more than one phone number in the way you're suggesting, like a chain store with a central 800 number.
I think you're probably going to be ok based on what you're describing. However, if you want to be absolutely sure the tracking number isn't indexed, I would recommend hiding the tracking number using either a JavaScript swap for search traffic or by making the tracking number an image. I would also be sure that the actual contact page for the location (if you have one) is using the local phone number you want indexed.
Hope that helps!