Hmm it looks even odder right now. I think the counts of charging ports were just fine. In your new version your Mk2 charges up to 12 bots which means (having infinite bots waiting for recharge) 12x2MW=48MW of energy demand, which isn't met by the internal buffer rate of 8MW, meaning at some point (a quick one) charging will take 6 times longer. If you have a look at the vanilla p.roboport you can see that you can have 2 bots charging at a rate of 1MW while the internal buffer rate is at 3.5MW, so you still have a surplus of 1.5MW, so providing enough energy to the system will recharge the roboport even when the max count of bots is leeching energy.
My suggestion would be to tweak the count of charging ports again (maybe even reducing the count of roboports), but setting the input_flow_limits to chargingports * chargingenergy * 1.75 (depending on how you want to balance it).
Hope that I do not annoy you. Cheers!