So what. Unless there is some net migration of passenger cars from one state, thru another, and to a final one, each state just concerns itself with collecting revenue from its residents who benefit the most from their own roads.
As for long-haul trucks which put a lot of wear and tear on multiple drive-thru-states, well, they are already tracked so it would be easy to proportion out their mileage and pay accordingly.
And if you just REALLY need to collect a few extra bucks from those freeloading cross-state passenger car drivers, add a special tax on highway charging stations. Don't want to charge locals, scan their license to waive the fee or even just base it on their CC info when they swipe. Worried thru-drivers will drive to a non-higway-taxed meter, then charge it on all meters with a provision to give locals that discount.
Problem solved, no special tracking meter needed.