I always wondered about this. While I understand for the most part, border control and right of military acess wasnt a thing, but Im preety sure I did something gamey when my polish ally calls me to club some lithuanians in the head, and I sail from Jerusalem, come ashore in Romania, cross all of Cumania, go stright through Kiev and finally reaching Poland, and nobody seems to be too bothered by 7500 frankish crusaders marching through heathen territories.
If Paradox didnt want to implement military acess so portrait the medieval situation (even tough nobles did send envoys to negotiate rights of passage, which was usually an expensive request), I wish they would create a modifier that would slowly drain your money when your non-crusading army marches into neutral foreign territory, to account for bribes and such.