If you're sighted in at 25 yards, you very nearly have a zero at 50. A ballistics calculator shows that a CCI SV round that's zeroed at 25 will be just over 1/2" low at 50 yards; a CCI Mini-mag 40 grain round will be about .15" low at 50. This is with a scope that is 1.5" above the center of the bore. That may be close enough for gophers.
Ballistics charts show how a trajectory should be when the bullet behaves according to known inputs such as MV, scope height above bore, and even wind and temperature. The barrel length is irrelevant. Why? Once a bullet leaves the muzzle it's flight is unaffected by the length of the bore it passed through on its way to flight.
With .22LR ballistics charts can't account for things that can't be given as an input. For example, any imperfection or irregularity in the bullet shape (particularly the heel, which is always unseen by the shooter), center of gravity, or weight usually remain unknown to the user but they can affect trajectory. Imperfections such as these are among the reasons for .22LR bullets not always behaving as ballistics calculators predict.
As for bore sighting at 100, next time anyone is shooting at 100 yards, take the bolt out of the rifle and look down the bore. A 8.5 X 11 paper wouldn't be all that easy to make the center of what is seen through the bore. Perhaps it can be done but it wouldn't necessarily be a simple thing. That's why a lot of .22LR shooters sight in at closer distances before moving to 100.