For those for whom email is flowing and are simply concerned at the reapplication of TMG policy, there is a setting in the troubleshooting node of TMG that allows you to disable email integration - essentially preventing TMG from monitoring and overriding config changes in Exchange / FSE.
I too am suffering this problem - I dared to add an entry to the FSE backscatter excluded domains list - and TMG has been offended ever since! Curiously, I can see in the logs that the transport config IS being updated every few minutes, but I have no idea what these config changes are, as it doesn't seem to be exposed in the log.
While not an effective solution, hopefully this is a viable workaround for some.