When you put it in gear you load the engine. On my 2003 it sounded like a quarter hitting the windshield. But only made noise under a load and with a MT it was rough to load it. Found a bent pushrod that was rubbing, low oil pressure, and a bad sleeve that was moving in the cylinder. After a rebuild the sleeve problem showed up as it still knocked so we used a different block.
UOA and looking at the oil filter media will help with a rod knock concern.
Your noise sounds like 1/2 crankshaft speed. So focus on powerstroke or camshaft related. May have to cap off injectors to see if it's a specific cylinder.
Not sure there is a good way to inspect flexplates without "while your there replace it" pulling the trans. Borescope (or thin USB) camera may or may not see a crack.