The NZGD49 datum is considerably less accurate than modern survey equipment. In particular it contains scale errors of several part per million.
SNAP can include a reference frame scale error into the adjustment. In effect this allows all observations which define scale (distance observations and GPS baselines) to be scaled to be consistent with the datum.
The reference frame scale error is applied in addition to the GPS reference frame scale or the distance scale error that may apply to the data.
You can either define a value for the reference frame scale error, or you can let SNAP calculate the value best fitting the data.
The reference frame scale error is defined by the reference_frame_scale_error command in the SNAP command file.