Are the bolts to the torque converter tight? I don't see what they would be able to rub on unless they were starting to loosen themself.
Mine started making a loud knocking/rattling sound from the same area and I too immediately thought it was a rod knock. Everything is so close together down there it's hard to pinpoint the sound. Once I got underneath and saw the flexplate I knew I found my problem. Not just one crack, there's cracks all over it. My sound is intermittent like yours, it seems like when it's cold it's quiet or barely noticable, but once it warms up and the metal expands it sounds terrible, like something is ready to let loose. Sometimes putting it into gear makes it worse, sometimes putting it in park makes it worse, it just depends on the mood.