I don't know about that business about Flea being the boss in this matter. Not saying you're wrong, just saying I don't know. I also don't know who makes what decisions in that band about stage amps (selection and usage) and whether they're made on a scientific basis, i.e. taking the entire system into account.
Good questions. Given that he's using in-ear monitors (as seen in the vids), I wonder to what extent he's relying on the amps for monitoring. They're all seasoned pros in the band, and could also be expected to have a top notch audio crew, so I'd be surprised if excess stage volume and the corresponding FOH interference is the issue -- but who knows?
If he's mainly using the cabs to hear himself, I think they're setup improperly: Flea is moving a lot off-axis, and he's running three units side by side -- not a good combination, since the wider the array, the narrower the dispersion. The proper way would be to cross-fire.
The dispersion remark holds true for direct radiators as well, but I think more side-lobes, potentially helpful in this case, can be expected due to a different velocity distribution across the combined source surface (array of smaller pistons vs large horn mouths with non-constant velocity across the section); horns tend to have a more controlled beam. Perhaps BFM can fill us in here.
Then again, the switch could be for entirely different reasons; changing matter of taste, loyalty towards the old trusty brand after a brief love affair with the blue beauty, maybe even a renewed megabucks endorsement deal from GK (probably unlikely, but again, who knows?), logistical problems, just a taste for variation, ...
I figure that chances are that we'll hear it from the horse's mouth sooner or later. Flea is of course interviewed every now and then, and this question is bound to come up.