I have the clunk occasionally and do not use the auto hold feature. Interesting observation, especially since this clunk seems to have occurred since the introduction of the Ford 10 speed transmissions in 2017.
The seatbelt warning drives me nuts too. Kinda SOL for stop-start on new vehicles. EPA no longer gives emission credit to car manufacturers for it, so maybe we will see it disappear.
According to a post on the 14th Gen F-150 sub (10r80 trans), Ford says its inside the CDF drum and on startup the clutch turns causing a clunk. Don't know if that is true or applies to the 10r60, but thought it may be useful.