That is the case here, that bolt goes through to the water jacket, thus the need for a sealant of some sort.
Some of the bolts penetrate into the jacket, not all, in fact none of mine do. I don't use anything on the bolts and they are fine.
On mine the inside bolt of the tensioner on the throttle side of the crank doesnt go into coolant, it taps into oil. I have to use yammabond sealant....nothing else will hold. I sincerely think this was the bolt they tried to identify that needed sealant and the one for the cover was a mistake