1. Minor differences in the shape of the tuners isn't going to make the bass sound different.
2. The bridge is the same.
3. The difference in neck shape on a '66 and a '72 are insignificant, and won't affect sound or playability.
4. The fretboard material is different? Really? Rosewood is rosewood, last I checked.
5. poly vs. nitro finish won't change the sound.
6. The pickups are the same Fender split humbuckers on both basses.
7. "Possibly" different body woods? Really? So the body wood on the '72 could "possibly" be better than that on the '66??
True, and functionaly speaking my SX is the same as my 64 Fender, but they aren't the same.
A C neck has a very different feel than a B neck.
A 72 has a fairly good likelyhood of being Ash. A 66 is more than likely Alder. That is certainly different.
There are differences in the pickups. There are differences between a 72 and a 2008 too, but they are both Fender split coils. They do however all LOOK pretty much the same. For that matter a mid 90's MIM split coil is still a Fender split coil too, but not the same.
Rosewood is Roswood? Better check again. Brazillian Rosewood, is different than Indian Rosewood.
The bridge is the same design (and so is my SX bridge) but there are differences in the saddles, so no, not the same.
The tuners work in completely different directions, so no, not the same.
Nitro vs. Poly has been debated at lenght. Regardless of personal opinions on the subject, you can't say they are the same. They are by design different.
Yup, lots of small differences.
So yes, functionaly speaking a 59, 66, 72, 79, 09, and and SX SPB 62
are basicly the same.
That said, my SX does sound remarkably like 64 Precision.

.. but they aren't the same.