Permits for overlength are not permanent, to the best of my knowledge, and are not reciprocal. They're a one-time use thing, and you need to file for one in every state you'd travel through. So every time you wanted to venture into a state where you were overlength, you'd need to apply for a new permit. Terribly inconvenient.
You could take your chances and roll the dice that an LEO or DOT officer won't pull you over and make you hold a tape measure. Since you're an RV, and as long as it doesn't look hinky from a distance, you probably won't get hassled. Probably.
A separate brake controller for each trailer is a necessity, because the brakes don't behave exactly the same on each trailer. You can try to adjust the brake shoes on each trailer so the same amount of power from the controller to each trailer will cause proportional braking, OR you can adjust the shoes properly and use separate controllers to tune each trailer's reaction to braking.