I think the keys are mouth size and tank niche. I had beckfordi and marginatus in with Apistos when I used to breed them. I had no problems. The niches are different, and the pencils weren't effective fry eaters.
kubotai? Good question. I don't keep Asian fish, but they look to me like fish that stay midwater or lower, and those I never combine with dwarf Cichlids. I have a 20 gallon tall of Nannostomus marginatus and rarely see the pencilfish below the top six inches of water. They like the surface zone in this single species tank, and that makes them reasonable companion fish for Apistos. Any mutual hatred is weakened by their rarely meeting.
To me, a good companion for Apistos has to be small, fast and not interested in the bottom half of the tank. It has to have a small mouth.
Cardinals and neon shaped bottom half of the tank fish have picked off fry here, even if they have smaller mouths. Cory group fish have been painfully harassed, and should never be in there. Pencils have had a nice balance of ease of escape, but limited 'crimes' to escape from.
I've had eques with Apistos too. And then, with time, I started prioritizing the 'dithers' and lost interest in the Apistos...