If you check the torque required to loosen most bolts including the cam caps with a torque wrench after they were correctly installed and have been in use for 5 hours and/or 5-6 heat cycles or more, they will universally indicate far more than the specified torque was needed to break them free. This is completely normal, and I fail to see how you, or anyone, for that matter, is or was able to determine whether the bolts were overtorqued from the factory.
Also very questionable is the idea that one can use a feeler gauge to determine accurately the difference between .10 and .09mm. That's .0004"
In any case, would be no need to shim to the wide side of the spec in most cases, since the OEM
installed shims are quite often odd sizes used by the factory, and if you just can't get Yamaha
shim in an increment of .05mm that makes you happy, you can used Honda
shims, which are sold in increments of .025mm instead.
It's also not that critical in the first place, since the difference between the min and max spec is only .002".
Still, it's an interesting tale, and it makes some sense to try reseating/retorquing the caps in the event a low hour bike is off by .01 or .02mm. Can't loose more than a little time by trying it.