Altimeters convert pressure variation to an altitude/eleveation reading based on an assumed model of the atmosphere.
A QNH set at a high elevation will mean that there must be a larger column height of this 'assumed model' of the atmosphere ie ISA with all its specifications.
The greater this assumed column then the greater the deviation from that day's actual column of air commencing from S.L. The altimeter is calibrated at ~30'/HPa but that isn't necessarily what a column of air extending from S.L. may have on that particular day.
The low elevation QNH has a shorter column of assumed lapse rates than the high elevation with the margin of deviation reducing the closer the elevation is to S.L.