It can be really hard to diagnose a problem if it only happens occasionally and it never seems to happen when the service manager is doing the test drive!
We will assume Cottman checked the atf level again yesterday as well as the fluid's consistency and smell and found no problem such as burnt or foam there.
Hopefully you mean to drain the fluid in the pan and change the filter not a 'flush'. Most autoboxs now have one-way valves in the system and the 'flushes' promoted by the quickie-lubes attempt to back flush the system which is either ineffective or will damage the system. And well ..... back flushing is not recommended by any of the manufacturers.
While you have the pan off you may consider adding a drain plug. It makes fluid changes as easy as an oil change.
I'm not sure what effect the exhaust might have although I am wondering if the exhaust problem night be the cause of the 'transmission' noise.
I've had pipe joint failures, pipes rust/rot out, mufflers rust out, and one that the end seams (crimped) failed and the end flap would flex out at certain RPMs They all have their own characteristic noises but generally all get louder under load.