A cracked flex should have been found during a trans install and would/should have broken and caused more issues after two years.
Being a noise you hear and can repeat, that helps. Can you hear the rattling when the car is in park at all?
It would appear to be driveline related if you hear it as you describe and only putting in neutral/accelerating changes it.
I assume they've looked at axles, wheel bearings, sway bar/end links (which is very commonly sounding like you mention) and backing plates?
