I can not really speak for other parts of the world, but in the Netherlands a fort did really stop such an army from moving, because going though the fort or the city was the only way to get from A to B.
Unless you wanted to move across a shallow lake, marsh or other bad terrain.
Take for example Groningen, access to the city itself was possible only by a few ways, sealing off each entrance would mean there was no way to get to the city. Sieging it took a long time, longer than what is portrayed in EU4.
Same for Friesland. You could of course land an army on the shore, but that was only an option when having knowledge of the waters and when controlling a nearby port where the ships could dock (needed to unload cannons, horses, supplies and basically all the men). From land Friesland was hard to reach, cause of swamps and lakes.
Holland, when land was flooded, was just insane to conquer, you could take a few cities, but first you would have to get passed so many barriers and other provinces...
A fortress in EU4 being impassable does make sense.