You just need to give a new mobileprovision file every three months, no need to update the app unless necessary.

I've always found it to be quite weird that the App Store is so closed, but a person with a developer certificate and MobileProvision can install whatever he wants and can do whatever he wants so long as the apps are codesigned. $99/yr is less than a couple coffees a month (or a good sushi plate) and way less than your phone bill, and is quite worth it for the bored hacker who wants to keep the warranty.