Many heavy-duty transmissions like the 5R110 have a built-in bypass filter. I know Jon's F-250 does. It is something like a 1-micron filter, absolutely ridiculous. The one he took out of the truck when he first got it was PITCH black. It kind of reminds me of a TP filter? Very odd looking. And since it is a bypass filter, it has no effect on the volume of fluid the transmission sees.
I've been trying to find out if the same setup is able to be installed on the 4R100.