Good theory, generally not even remotely an issue on a TJ.
What material do they use for galvanizing fasteners?
Typically zinc. The zinc isn’t necessarily intended to encapsulate the base metal. Instead, it is intended to corrode prior to the base metal.
Zinc plating, when the fastener is fully encapsulated, does indeed protect the fastener from corroding for quite a long time.
But even if the plating is chipped or damaged, as often occurs when a bolt is threaded in and torqued, or when installed/removed repeatedly with an impact gun or socket wrench, the zinc plating will still protect the base material, and in many cases, the surrounding material. At the location of the chip, the exposed steel does not rust, because the steel bolt base metal and the zinc plating create a galvanic couple. The zinc begins to corrode, but as long as there is adequate surface area on the zinc, the steel does not corrode in any significant amount. However, in this case the zinc plating is being consumed, and the time the fastener will survive is limited.
Keeping the plating encapsulation intact does indeed extend the life of the bolt. Every chip, scratch, or grind mark cuts the amount of time the bolt has until the plating is consumed, and the bolt itself corrodes. The rate at which the plating corrodes is dependent upon the surface area of the exposed steel (for small steel:zinc surface area ratios), and thus the more zinc is chipped off, the less time the bolt has until it begins to rust.
You can experiment with this at home. Get a bucket of salt water, and a lid. Get a few bolts and nuts.
Start by throwing a brand new zinc plated bolt in the bucket. Next, take a zinc plated bolt, and grind some of the plating off on the head. 3rd, take a zinc plated bolt and screw on a stainless nut (316 for more dramatic effects) tightly against the head. Finally, throw in an aluminum bolt with a stainless nut tightly screwed on. Make sure none of the bolts touch each other in the bucket. Throw a lid on, and let it sit for a long time.
If followed correctly, there should be little to no change in the plated fastener. Since the base steel is fully encapsulated, no galvanic corrosion can occur. The steel is simply not exposed to the electrolyte.
The plated fastener with the grind marks will at first begin to lose its zinc plating, and once sufficient plating is lost, the base steel itself begins to rust. Unlike the previous bolt, both the zinc and the steel are exposed to the electrolyte, and galvanic corrosion occurs, consuming the zinc. Once the zinc is consumed, the base steel now will corrode via non-galvanic processes.
The zinc fastener with the steel nut will be even more interesting. Even though the base steel is still fully encapsulated, the zinc and the stainless quickly create a strong galvanic cell, resulting in rapid loss of the zinc plating. Once sufficient zinc is lost, the base steel becomes exposed, and the carbon steel and the stainless become a secondary galvanic cell, resulting in rapid rusting of the newly exposed bolt.
The aluminum bolt and stainless fastener is a wild card. Aluminum and stainless will indeed form a galvanic cell, but depending upon the exact specifications, the aluminum could passivate, or essentially corrode a layer onto itself that actually protects it from corrosion. In other cases, passivation will not occur, and the aluminum will corrode through. Any hairline cracks in the aluminum will result in corrosion in the crack, significantly weakening the material. In combination with repeated stress, this results in rapid fatigue cracking, known as stress corrosion cracking.