If there's no fort in the province, it makes sense to me: the rebel army springs forth because the province itself is in rebellion. That means that the province itself should start rebel-occupied, unless you own a fort there.
If you don't want to suffer the on-siege-won effect, either build a fort next to it/on it, or use harsh treatment.
If armies are unable to deal with rebels then why do I get an -unrest bonus when I have an army there? Clearly they are useful for supressing rebels. No one can occupy a province while there is an army defending it but rebels can? Why?
And there are a ton of random events that spawn rebels that you cannot really foresee. I cant just build a fort there within 6 months. Theoretically from a design perspective you couldnt even wait and just unmothball forts while the event window is open. (doing things while there are serious events happening is arguebly a bit gamey) So you basically have to have your forts unmothballed unless you want some random event to convert your province and there is literally nothing you can do.