Just heard from BMW. An Engineer Specialist was in the shop and they had him take a look at my car. Turns out that the Transmission is making a noise that is echoing up the engine and giving the illusion of rod knock. I pick the car up today and they call me to bring it back in a few weeks.
The part is custom ordered from Germany and shipped over. They'll drop the tranny and install the part. From what it sounds like the part is just a dampener because there is actually nothing wrong with the tranny, there is just something that is knocking. :-/
They also identified some other minor issues, like coolant leaking from the reserve take for example, that they have addressed already.
He said that they can't be 100% sure until the part is installed and they listen for the noise again, but he said that off the record he is 100% sure that this will solve the issues. So for now we will all assume that we found the issue and I'll re-bump this thread in a few weeks if it turns out to be something different!
2015 M3 // Black Sapphire Metallic / Black Extended Merino Leather / Carbon Fiber Trim / Executive Package / M Double-Clutch Transmission w/ Drivelogic / 19" Black Light-Alloy Wheels / Adaptive M Suspension / Harman Kardon surround sound
Other // Shell Rotella T6 5w40