It only makes sense to modify the diameter of a tone hole, when the note produced by it has the same kind of deviation in both registers.

That's certainly not always the case. Also, the magnitude of a deviation has to be larger than a 10 cts. to yield an audible need for adjustment. Measurements certainly are essential prior to any modification. Key height also cannot be neglected – not only in relation to the pitch produced, but for sonority as well. These two aspects have to be considered in relation to one another.

A tone hole that's too large can be amended by inserting a ring or a crescent into it and this can be done without any harm to the the instrument as such – a tone hole that's too small sometimes can be reamed a little, but in more serious cases it can only be enlarged by fitting another and larger soldered-on tone hole in its place.