Okay, maybe this is the final word from Fender regarding different sized pickups in Fender MIM Jazz basses, when the change occurred, and with what kind of pickups.
After all the discussions on another thread, and sidebar discussions regarding hum-cancelling, I sent Fender an email with a few very direct questions. Here is a summary of what Fender emailed me back with... I guess I would consider this an "official" a response as they will ever give. I am not a luthier like SGD Lutherie or walterw (from this forum), so I can not vouch for the accuracy of the physics, but this is what a "Supervisor of Production" at Fender said:
Regarding MIM Fender Jazz basses:
Before 2001 = 2 pickups of same size with flat poles (i.e. identical "neck" pickups wired as neck and bridge) as a cost-savings measure. These are considered hum-cancelling if volumes are kept equal (not the volume pots---the actual produced volume--explained farther along). The lesser quality of this set up partly stems from the fact that the "bridge" pickup magnets don't line up well with the strings as they spread apart as the strings approach the bridge (because it is not wider). This gave a different volume to the "bridge" pickup vs. the neck pickup when the volume pots are set at the same levels (but doesn't affect tone). So players would have to either turn down the neck pickup or turn up the bridge pickup (relative to the other) to try and balance them when hum-cancelling was desired. Since most jazz players know that turning the volume pots both "full on" cancels hum (from experience with Fender MIA jazz basses, among others, which had different sized pickups), they would try it with the MIMs, but it didn't work on these. This is a pain, and if the volume settings got bumped once set to hum-cancel, you'd have to readjust them. Fender was okay with this until the popularity of the MIMs and the demand by its customers to produce a more universal pickup size and sound brought about a change. Comment: I would think a simple calibration of the volume pots to make the knob settings and the actual volumes equal between neck and bridge would fix this problem, but maybe this wasn't practical given the QC at the Mexican plant (?).
2001 and after = 2 pickups of different sizes with raised poles (i.e. true neck + bridge pickup, and humcancelling when volumes set equally) is the norm. There were a few 2001 runs made with 2 different sized pickups with flat pole pieces when the raised weren't available due to limited supply early in the production change. These are considered of a lesser quality than the pickups with raised pole pieces, and are "very few in number" (no specific numbers given). It wasn't stated if these were hum-cancelling or not, but I would guess they are. These "flat pole pickups" would have a different sound vs. the raised pole pickups since the distance of the magnets from the string varies the volume of that string. So you get a different "blend" of individual E+A+D+G string volumes with a flat pole pickup vs. a raised pole pickup. Since the new "raised pole" pickups were wider at the bridge, they line up with the strings better and pickup equal volumes as compared to the neck pickup. So any time the volume pots are set equally--the easiest of these settings is both "full on"--you get hum-cancelling. Thus these work similarly to MIAs or any other jazz bass with 2 different sized pickups. The quality difference is in the wire and magnets used in MIMs vs. MIAs. It would be very unusual for any 2001 MIM Fender bass to be seen today with 2 different sized pickups that have flat poles... Comment: I guess they are that few in number and most have already been modified.
So, according to Fender, if you have a Fender MIM Jazz bass made 2001 or later, you will (should) have 2 different sized pickups (with raised poles) and if you want to swap them out, any standard sized neck/bridge jazz pickup set should fit without any modifications to the body or pickguard. If yours is made before 2001, you will likely need to do a little routing to make the bridge pickup fit. (Note: these dates are not consistent with what I was previously told by a Fender tech, but does seem consistent with what TB members say)

After all the discussions on another thread, and sidebar discussions regarding hum-cancelling, I sent Fender an email with a few very direct questions. Here is a summary of what Fender emailed me back with... I guess I would consider this an "official" a response as they will ever give. I am not a luthier like SGD Lutherie or walterw (from this forum), so I can not vouch for the accuracy of the physics, but this is what a "Supervisor of Production" at Fender said:
Regarding MIM Fender Jazz basses:
Before 2001 = 2 pickups of same size with flat poles (i.e. identical "neck" pickups wired as neck and bridge) as a cost-savings measure. These are considered hum-cancelling if volumes are kept equal (not the volume pots---the actual produced volume--explained farther along). The lesser quality of this set up partly stems from the fact that the "bridge" pickup magnets don't line up well with the strings as they spread apart as the strings approach the bridge (because it is not wider). This gave a different volume to the "bridge" pickup vs. the neck pickup when the volume pots are set at the same levels (but doesn't affect tone). So players would have to either turn down the neck pickup or turn up the bridge pickup (relative to the other) to try and balance them when hum-cancelling was desired. Since most jazz players know that turning the volume pots both "full on" cancels hum (from experience with Fender MIA jazz basses, among others, which had different sized pickups), they would try it with the MIMs, but it didn't work on these. This is a pain, and if the volume settings got bumped once set to hum-cancel, you'd have to readjust them. Fender was okay with this until the popularity of the MIMs and the demand by its customers to produce a more universal pickup size and sound brought about a change. Comment: I would think a simple calibration of the volume pots to make the knob settings and the actual volumes equal between neck and bridge would fix this problem, but maybe this wasn't practical given the QC at the Mexican plant (?).
2001 and after = 2 pickups of different sizes with raised poles (i.e. true neck + bridge pickup, and humcancelling when volumes set equally) is the norm. There were a few 2001 runs made with 2 different sized pickups with flat pole pieces when the raised weren't available due to limited supply early in the production change. These are considered of a lesser quality than the pickups with raised pole pieces, and are "very few in number" (no specific numbers given). It wasn't stated if these were hum-cancelling or not, but I would guess they are. These "flat pole pickups" would have a different sound vs. the raised pole pickups since the distance of the magnets from the string varies the volume of that string. So you get a different "blend" of individual E+A+D+G string volumes with a flat pole pickup vs. a raised pole pickup. Since the new "raised pole" pickups were wider at the bridge, they line up with the strings better and pickup equal volumes as compared to the neck pickup. So any time the volume pots are set equally--the easiest of these settings is both "full on"--you get hum-cancelling. Thus these work similarly to MIAs or any other jazz bass with 2 different sized pickups. The quality difference is in the wire and magnets used in MIMs vs. MIAs. It would be very unusual for any 2001 MIM Fender bass to be seen today with 2 different sized pickups that have flat poles... Comment: I guess they are that few in number and most have already been modified.
So, according to Fender, if you have a Fender MIM Jazz bass made 2001 or later, you will (should) have 2 different sized pickups (with raised poles) and if you want to swap them out, any standard sized neck/bridge jazz pickup set should fit without any modifications to the body or pickguard. If yours is made before 2001, you will likely need to do a little routing to make the bridge pickup fit. (Note: these dates are not consistent with what I was previously told by a Fender tech, but does seem consistent with what TB members say)

if new pickups won't fit.