As you know, there are two pumps; one for the engine, and one for the transmission.
The filter is place between the engine oil pump and the engine (most of it anyway). The trans does not receive filtered oil; and the mainshaft and countershaft don't either.
Obviously, the engine oil pump pulls oil from the common sump, so oil in the filter could be from any engine/trans component. There's not much between the pickup and pump.