Working on my M35A3 with the AT1545 it was explained that the pump feeds the valve body and clutch pistons, then goes to the torque converter, then out to the cooler and feeds back into the tranny which lubricates all the bearings. In my case, a worn input hub on the torque converter could let fluid leak and then the pistons will not hold, burning up clutches. Burned up clutch will generally not pass the filter but any debris that gets out of the torque converter will contaminate bearings and or deposit in passages.
So what we are worried about is keeping lube where it needs to be while removing the old. If there were a direct input to the pump and you had an elevated supply, that would seem to be the optimal solution. Simply putting fluid into the return line would seem to work, but it would mix with old fluid and there is no or little suction. Expecting it to siphon from a container does not seem to be a good choice, since there is no actual suction where the return line puts it into the tranny.