The only way a bomber can transport a paratrooper or an infantry unit in the mechanized phase is by using the optional rule. Otherwise you can't paradrop or air transport in the Mech phase.
Per the optional rule, for a paratrooper to move during the Mech phase, neither the paratrooper or the bomber conveying him could have moved (and add "participate in combat") during the regular movement phase.
Otherwise wacky things can happen that are impossible to plan against. . .