If indeed some B/W OD’s have different fill plug heights, possibly so a general instruction covers all models?  Regardless, if overfilling the trans (by reinserting the plug before the OD level had fully dropped) resulted in clutch contamination, wouldn’t that verify the manual was in error?
More than likely though, the ‘OD first’ order was probably designed to prevent overfilling/clutch contamination.  Too many guys would fill the trans first, plug it, and then fill the OD.  By filling the OD first, they must have assumed that by the time the trans got filled, enough excess would have drained to insure a common/safe level.

6 VOLTS/POS. GRD. NW INDIANA