I guess 6400 is the highest sensitivity that the sensor is capable of. Anything higher is probably based on processing, maybe too much processing for ISO-Auto mode. So I would probably avoid ISOs higher than 6400 when selecting ISO manually as well.
I know anything below 200 or above 6400 is pull or push on the E-M1 mk II. But actually on my E-M1 mk 1 and E-M5 II 6400 is already marked as 'Extended' if I change iso in the super control panel. And yet I can set 6400 and higher as a high limit in the ISO-Auto Set menu for the older cameras but not for the newer one.
As for using iso above 6400, sometimes I find myself taking photos of my kids running around and I need a shutter speed above 1/250 whatever the iso may be.
Do you have an external hot shoe flash (besides the little one that came with the camera)? That might help especially if you bounce it off the ceiling so you don't get that "onboard flash" look.
Since the camera is limited you to 6400, one possible quicker solution is to drop the camera into Shutter Priority mode, pick the shutter speed you want, ISO will peg at the 6400 max, and take your shot. Of course it will look very underexposed, but if above 6400 is simply digital amplification, then you can apply the same +EVs on the computer. Not really the best solution, but if it allows you to quickly get the shot a bit faster than if you have to drop into "M" mode and potentially adjust all three settings (S, A, and ISO). it might be something to try.