Sometimes when I've needed to calibrate my Altimeter, it's often been indoors which means that it can't get the altitude from the GPS.
However, I live in The Netherlands where almost all of the country is below sea level. This means that if I need to manually correct the altitude, I need to climb to the top of my house in order for it to be 0m (which is the lowest that manual input can go) in order to calibrate it correctly.
Calibration via GPS of course sets the correct negative value, it's only the manual input that does not go below 0m.