Although the KC-46 systems problems certainly don't bode well for the whole fiasco, the above is not why Boeing won KC-X.
Basically, there were three competitions for KC-X. The first was the one that Airbus won. However what GAO said in reviewing the protest was
not that Boeing OR Airbus had the better plane. They refused to even rule on that. What they said was that by USAF's own specifications, weightings for ranking and their own rules for evaluation, the award to Airbus couldn't be justified as announced. They stated that USAF needed to explain how under their own rules, how they could make the award they did. USAF didn't even try and so the contract was canceled (no doubt with penalties awarded to Airbus). Basically, USAF said they wanted one thing, then decided they wanted something else and rather than just issue a new solicitation, twisted their evaluation to get the result they now wanted. Boeing didn't win on every complaint but did raise the point that if USAF had asked for what they were eventually desiring to begin with, Boeing would have bid a "KC-777", which may or may not have won.
The second contest was very short because it was clearly loaded for Airbus. Among the things done was that requirements where the A330 had fallen short were changed or simply eliminated. And, as a kicker, the time for bid was shortened as was the required development time. This would make any "KC-777" bid be deemed too high risk. This became so obvious that the second competition was aborted and never hit the street.
In the the third case, the requirements that finally came out (Boeing said it wouldn't decide on a KC-767 or KC-777 design until they saw them) were much closer to the original requirement, the larger load options would be requested in KC-Y or KC-Z. Boeing apparently lowballed, possibly thinking the big profits would come down the line, but it's likely they still would hae come in lower given they were starting with a KC-767, which was smaller and less expensive that the A330 base airframe.
Now it's just my opinion, but with eh crazy way Air Force was awarding and managing contracts at the time, Airbus would have had problems too. The KC-46A is based on, but not the same as the KC-767s offered for export earlier.
