Just to be clear, there is no rudder to kick out in the flare, there is a crab angle, in coordinated flight, which must be reduced to runway alignment using rudder for longitudinal correction while using aileron to keep the upwind wing from rising due to the yaw. This crosscontrol in the flare is also be called a slip.
Any aileron input error should be to the excess which would put the upwind gear down earlier than the downwind. Some guys do that on purpose.
I've seen more sideslip to landing sideloads on big jets caused by the guy who wants to fly it like a cub than sideloads by guys who did not decrab enough.
If your airplane does autoland read how it corrects for X-wind.
Even on aircraft designed to land in a crab, such as the T-38, most guys naturally gravitated to a decrab in the flare.