I wonder what companies will do now, probably embed the tracking information within the URL without using parameters, like dynamic URLs that are unique to a particular user/cookie?
EDIT: They could also do something similar to what they've done with Content Blocking Extensions, maybe call them "URL Cleaning Extensions", which allow third parties to maintain tracking URL pattern lists which Safari can then follow to do its unwrapping.
When the web server gets a request, it can validate & decrypt, update any tracking values, and redirect to the real URL.