I don't have any more solid or useful input than to agree with the above, that the random commanded AFR dips are just an LSJ thing that we can't see and/or can't control in HPT. The P12 is not very well supported.
I will add, I'd come across clues in various LSJ tuning forums that linked commanded AFR dips to misfires, and to maxing out the COT threshold table. I was having some idle misfires due to an idle RPM target of 800 which was just a little too low for 80# injectors, even with a BRFPS. Bumped target idle up to 900 and the idle misfires went down as did the commanded AFR dips. I will soon be trying some changes to the COT threshold table that I've seen elsewhere, where the adders are zeroed out but the thresholds are not maxed out (maxed out shown, other tunes I've seen have all the threholds at 2200).
One more point regarding living with the bugs, it does not appear to me that super rich commanded AFRs throw off fuel trims, if you're doing fuel trim tuning, and it shouldn't throw off WB tuning either. If it's commanding 10.10 AFR like mine did and the WB is reading 11.11, that's still 10% rich for that point on the VE or MAF chart, and that can be dialed in.
Where are you seeing whack commanded AFRs, at idle or elsewhere?