How much atf is needed for my truck?

I have a 2016 4x2 2TR-FE 4cyl. AC60E Transmission.

I downloaded instructions on doing a tranny drain and fill and the instructions say to use 1.6 qts. When I filled it cold I drained around 1 qt cold out of the tranny but it took 3.2-3.3 qts before it started coming out of the overflow plug. I then got it to temp by jumping the OBD ports and drained the expanded fluid from the overflow plug.

Should I do it again but just use 1.6 qts this time as the manual says to do? I don’t get why this says to only fill 1.6 qts when the pan clearly holds more fluid.

 

You stated the answer to this yourself, expansion. The fluid needs space to expand when hot or bad things will happen.
I would let the truck sit overnight and do the check procedure tomorrow from the beginning, then you will know if you are still too high or too low.