Actually, the engineers build that added tolerance into their Valve Clearance Check specification range. That is why if all of your valves are within the defined spec range (even at the minimum) you are safe to go another 26k mile interval to the next check. No guarantee that they will still be in the spec range after that additional interval, but they will still be within safe operating range (which is greater than the clearance spec range).
As for why everyone wants then to be in the middle? I don't. I want mine in the 70 percentile to the open side just as Billy Yamafitter's Most Excelletnt Valve Shimming Spreadsheet calculates it.
Why do I want that? Because valve clearances always shrink as they wear due to eroding valve faces and valve seats. There is no significant wear to valve stems so they never get shorter and cause an increase in clearance. The only thing that could potentially wear and increase clearances is the cam lobe or bucket followers, but those are very hard pieces of well lubricated steel. No, if you see the valve clearances increasing it is because of build up on the valve faces or seats, not wear.
So knowing that the clearances will get smaller with wear over time, and that the problems that one potentially faces with their valves is when the clearance shrinks to the point where they no longer can close completely, biasing them on the larger side of the spec range will buy you more time between required valve re-shims (not valve checks, they still need to be done per Yamaha's 26k schedule at a minimum).
Yes, I realize that the valve lift (and duration) is lessened somewhat by the amount of the increase in clearance. That amount of difference is insignificant. Follow along now...
Both the intake and exhaust cams have the same cam lobe profile dimensions. Their total theoretical lift (difference between the lobe dimension and the non-lobe dimension) is 8.053mm. So 7.9mm maximum valve lift (in round numbers) when you subtract the minimum required clearance (.15mm intake and .18mm exhaust). The spec range is a total of .07mm in both cases, so setting the valves to the ~70th percentile (open side of middle) is roughly .05mm larger than the minimum clearance specs.
0.05mm / 7.9mm * 100 = 0.63 %
That is how much difference in lift that you will experience by setting the valves to the minimum clearance vs. the 70th percentile open side of middle. Is it really worth it to anyone to have to re-shim the engine at every 26k mile valve clearance check in order to maintain that less than 1% potential increase in horsepower?
I say potential because I have not brought the valve duration into the mix since there is no way to know if lengthening the duration (and overlap) will increase or decrease the engine's torque, and at what rpms. That would depend on where the engine's valve timing lies in its stock form, but whatever that change might be, it would clearly be equally as insignificant as the lift.
YMMV
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