Personally, my explanation for the 1600-series clones and the "12 like her" line is this:
The 1600-series ships (and the 1017 Constellation) have been refitted to externally indistinguishable specifications. Internally, some have more or fewer weapons, sensors, automation, etc. Pike had a crew of 200, because he was a standard GalEx Heavy Cruiser, with a standard mission profile. So his ship was fitted out with the equipment he'd need, and a crew big enough for that job. A MiliOps Heavy Cruiser of the same type would have a larger crew (say 300?), more individual phasers, fewer labs, etc. When Kirk got Enterprise, she came out of a refit that gave him a ship loaded for bear - 400 crew and all the bells and whistles. You have to save volume somewhere, so he has fewer phasers and photon torpedo banks, but more sophisticated models - like carrying an M-16 while the Pike had the equivalent of 8 bolt-action rifles. The simpler model is larger, takes up more space, and has more redundancy. It's the tradeoff. Kirk's ship is part of Independent Ops, and can go anywhere, perform any mission. So, since only 12 or 13 are fitted out and assigned to Independent Ops, there's your "12 like her". But the NCC-1664 Excalibur can easily be a Baton Rouge subtype that's been refitted and refitted until it matches the Constitution class externally. Or as was suggested above, NX-1700 was a prototype, and still testing out the limits of the design, so 1701 was the first production model. And since a lot of designs get scrapped in design or testing, NX-1600 was a failure, and as more 17-series ships were needed, unused 16-series numbers were used. 18-series couldn't be used, because until (or if) NX-1800 is designed and built, we would be poaching their numbers.
Overall, though, I just don't see the need to follow the 17-01 logic slavishly. It's a kinda cool thought, at first blush, but once you start really trying to apply it, it falls apart and locks you in too much.