It does not have a cargo door nor a cargo floor. The KC-46 is derived from the 767 freighter and has both a large cargo door and a main deck cargo floor. So if cargo is priority for the user, A330 loses.
The A330 MRTT has underfloor cargo space for 45 tonnes of pallets (it can actually carry more cargo than the A400M). All of the MRTT's fuel is carried in its usual tanks, with no need for auxiliary tanks in either than main cabin or under the floor.
The KC-45 was to have a cargo door at the USAF's request, but that is not a requirement for any other operator.
By contrast, the KC-46A loses much of its underfloor cargo space to auxiliary tanks, and while the A330 MRTT can carry over 200 passengers the KC-46A is only certified to carry 58 (and has space for just 114 in its usual configuration).
The A330 MRTT is significantly larger than KC-46 and the KC-135. If the user has a large number of KC-135s and desires to operate the new tanker from the same bases as the old tanker, the A330 loses.
The KC-46A may have a very marginally shorter take-off run than the MRTT, when you take into account the actual length of runway required due to safe abort distances there is next to no difference as to the size of airfield required by both. Interestingly, the KC-46A will not be able to take-off from Mildenhall or Fairford with a fuel fuel load for this reason.
If fuel burn while orbiting and waiting to service receivers is a priority, the bigger airplane burns much more per hour than the smaller airplane. And so the A330 loses. Again.
I don't know the fuel burn figures for the KC-46A, but the A330 MRTT's is 4 tonnes per hour in the cruise and 6 tonnes per hour with the hoses deployed. I'd be surprised if the KC-46A was a meaningful factor less than this.
There are other "things" being installed in those airframes that have nothing to do with the tanker mission. Airbus simply could not do these other "things". And those "things" were yet another high priority for the KC-46's user.
Are you referring to the EMP hardening, ballistic and NBC protection of the cockpit? Granted, the A330 MRTT doesn't have that, but then no one has requested it.
I don't know the facts related to your other points.