Re: State border crossings, too
I first encountered the agricultural inspection stations about 1959. MedFlys were news maybe 30 years later. So I doubt that they were the impetus. If Doc Brown had an effective time machine it could perhaps have been better used _before_ they arrived en masse.
The point about "so many roads" could have some validity. The Rocky Mountains, Sierras, and similar do have the effect of funneling traffic through a very few crossings, making borders of any sort more cost-effective. In contrast, stopping all "smuggling" along/across the Mississippi River would be a lot tougher.