The 2-midnight rule applies to the hospital, not to the physician. (Also, the rule also means that the expectation is that the patient will require 2-midnights, not that the patient ended up staying that long, so a shorter stay does not necessarily disqualify the inpatient status.)
In the facilities where I've worked, the process has been to use the codes based on the status to which the patient was admitted. But in some instances, with short stays, the hospital may retroactively change the status from inpatient to observation after a review or denial, in which case it may also be necessary to change the coding of the physician claim as well so that it matches what the hospital is billing.