Probably has to do with when the forks were assembled.
When putting the fork cap onto the damper rod, part of the proceedure is backing the damper rod lock nut down the threaded portion a specific amount, spinning the fork cap down on the threaded portion, and tightening the lock nut up to the fork cap.
If one side is slightly off compared to the other, you get what you're describing because one of the clickers will be a bit further in or out to compensate for this mismatch.
I'd just screw both adjusters in to the max until they lightly seat (stop turning), not force anything, and back them out the same number of clicks.
If you want to get involved with the innards in an effort to make everything even-Steven, I'd check the fork cap assembly.
This is where the Yamaha Service Manual is worth the price.
I doubt your situation will amount to anything, myself.
Yes, the clicker pushes on a rod which makes for more or less oil flow.