No, that is not it. Although I appreciate your "theorizing" (I prefer the term outtermind-philosophizing, which is one of my unconcious hobbies).
The percentage means how many of the rocks you have analyzed, out of the total there is, not the total you collected. The many percentage miscounts - mostly in Collecting, but in some other skills too - happen after installing an expansion that adds to that total number of collectibles. Note that there are skill challenges (such as Collect 100% Butterflies) that do not count the expansion collectables, hence allowing you to get 100% from the base game, and then go further by getting the ones from expansion packs. I believe there was a patch that made it so that the numbers couldn't go any higher than 100, which is somewhat a rushed fix.