But who tells you "no"? The whole country is de facto under your control, what's preventing you from keeping anything?
What makes you think the whole country is de facto under your control simply because you have "occupied all the enemies provinces" (and likely destroyed all his regiments)?
1. You cannot build anything there.
2. You get no taxes or trade from there.
3. Occupied provinces count for zip when it comes to manpower, force limits, borders, etc.
4. If you go off and leave them be, rebels will spawn and return provinces to their rightful owner.
The only way that "occupied provinces" are a beneficial asset is in using them as leverage to convince a rival to accept your peace demands. Having 100% of a rival countries "provinces occupied" DOES NOT MEAN that you have de facto control of their country nor that they have zero chance or ability to resist your demands.
Rebels can liberate provinces, and those can be used to recruit mercs or muster new native regiments. A countries rate of manpower renewal is (I'm guessing) reduced for occupied provinces (if not eliminated) but the pool does not get eliminated. Also, if I am not mistaken, the enemy regime retains a portion of its tax revenues even from provinces that are enemy occupied, and there is virtually no impact on tech or diplomacy (apart from indirect effects from things like prestige). Hypothetically, a very popular and diplomatically influential sovereign could still kick your ass even AFTER you get them to 100%WS, though admittedly the chances of that ever happening seem to be slim.
People take the "occupied province" status far too literally. It doesn't mean WWII style total war destruction of all warmaking capacity and armed garrisoning of every single village and crossroads. Hell, you can siege an "entire province" into occupation with 2000 guys!? Even 1000 guys if you are talking about colonies pre rampart building.
"Occupying a province" obviously just means, you have taken control of one or two key strategic points (maybe a castle and a village that are at a travel nexus) and they have de facto lost control, but that doesn't mean that you have de facto gained control. You are simply denying control to them.