Manual tweaks would be nice.
How about a checkbox next to each band to "lock" it?
I was fiddling around with stacked subs yesterday and had limited the correction spectrum to 20-800Hz. The PEQ did a nice job of flattening and extending my response down to about 25Hz.
Then I did a full-spectrum pass and ALL the PEQ bands under 80Hz were reassigned to flattening my higher-frequency problems. Bass extension is now gone.
I guess manual adjustment using other SW (like REW) is the only way to get what YOU want.