The basis of the AF1 is 747-200, not the -300. I worked on the Air Force One project for Boeing in Wichita, Kansas for a few months in the late 80s. The AF did not want the 747-300 even though it was certified at the time of the bid proposal submittals. The -300 did not have enough service experience to meet the bid proposal specifications. The competition was between the DC-10 and the 747-200.
BTW, the only reason the 747-200 AF1 has in flight refueling capability is because the DC-10 couldn't meet the AF1 range requirement, so the AF revised the spec to require all bidders to include in flight refueling (and keep the DC-10 in the competition) even though the 747-200 did not need refueling to meet the requirement.