Transmissions when replaced will always come with a replacement torque converter along with them. This is because typically when a transmission fails it sends metal throughout the assembly. You can never really flush a torque converter in the shop well enough to prevent contamination from an old converter from getting into a rebulit or new transmission. So, they come with one.
I am a little miffed that they are estimating both a transmission and a separate torque converter. Why don't you call to verify that information - even try a second dealer for information.
Flushing the transmission fluid is never expressly recommended by Acura. Even as non-recommended proactive approach, I agree that it is probably worse to flush your transmission fluid at this time given your concerns. You may actually accelerate failure, as debris may move to a catastrophic location.