Flat response on an RTA is just, well FLAT and that doesnt equal good sound. Flat means every frequency is reproduced at the same level, so that nice 30-40Hz bass note, has to be at the same output level as 1K, I am sure your low end output exceeds the mid range

With your setup it would be very hard to acheive flat response with your subs set to their normal everyday output
I am sure Bob has a set of SQ and RTA settings that differ very much from each other. Most cars "back in the day" had 4 Audio Control EQT's (they are single channel) Two for SQ, Two for Flat RTA response. The EQT is a 30 Band EQ so they can tweak any freq.