Since the only person that I need to please is myself (from a system perspective), I did not feel the need to remeasure and validate my set up using the software.
Yes. While I can appreciate the logic behind what AM is doing, I think the final judge winds up being your ears.
Point taken @viridian. What threw me is that in past cart setups I hadn't been surprised like this. My Zephyr MkII was/is relatively quieter. I'll give it time after I feel I've gotten it tweaked properly in setup.