Opinion dictates how much of the non mandated levy is given to you. Church, city and feudal levy amounts are all set by different laws, same as taxes.
Just because a holding is in your county doesn't mean it is your vassal. Someone in the past may have transferred the vassalage of the bishophric to another noble, or it may have been inherited out of your vassalage. You can check a holdings fetalty by looking at the flag on the top right of it in the county view
After checking, it appears that a bishop can be loyal to three people: You, in which case you get the amount of levies that the law say you should get. Himself, in which case you get none (which is extremely odd and a bit nonsensical, especially if you are his direct liege lord). Or the pope, in which case you also get none (which is also a bit odd, since he can't ever actually raise the troops even if you declare war on him.
Larger levy laws only help you in a single case, and even then are a bit counterproductive (since if they like you enough you will get a significant portion of the levy anyways, but if they don't like you very much then you will get nothing no matter how harsh your laws are. And the harsher the laws are the less likely they will like you enough to give troops).
However, if a bishop IS going to give you troops, then he will probably give you more then a city because he already likes you a lot (and churches give lots of troops).
Finally, the description text on the church levy laws states:
The Prince-Bishops are expected to provide a [small/medium/large/whatever] amount of troops for the defense of the realm.
Which seems to imply that only Prince-Bishops are effected by the levy (they aren't actually, as they can easily be loyal to themselves too and give you no troops at all).
It's possible that my game has some large scale glitch effecting the amount of troops coming out of churches, but I doubt it (and if anyone really wants me too I will post screenshots of various churches and levy results and such, but uploading them is a bit of a pain, so unless someone specifically requests it I won't bother).