Manually adjust after TuneEQ is done? Besides the very limited options in the RTA settings, there isn't anything you can do to change how TuneEQ does its job, but once it does you could always go through and see if there are any filters you can combine/elminate to simplify the amount of bands used. Alternately, adjust the amount of bands used per speaker, ie for LH/RH i use bands 9-22, LM/RM i use 3-13, rear fill about the same, sub 3-9. This way TuneEQ uses less unnessesary filters, making the most out of the bands you choose. This way also leaves 3-4 bands you can use as per-side or global, after the FR per speaker looks good.
Or skip TuneEQ and import/export using REW's auto EQ. REW gives you total control over Q, amount of bands, boost, whatever you want