I think the reason for the change is mostly what they state, to be able to police the power unit. The gains of qualifying modes are simply a bit suspect. The intention of the rulebook is to have two sources of energy: the 100kg/hr limited fuel flow and the 4MJ from the battery.
In race mode the between engines are small, yet in quali modes 50 hp differences exist. With only fuel and battery as power source, that has to come mostly from fuel (assuming electrical eff. is pretty good and similar), and 50 hp would be more than 5%, pretty amazing at the high thermal efficiencies they have (e.g. 50 vs 53%), and why would the difference only be in quali mode?
So probably part of the gain is from loopholes in the regulations. A bit of fuel accumulation, a bit of oil burning, etc. FIA wants to shut that down, and since they cannot police it, they simply ban quali modes.
Yet to have a sensible racing engine, I think you need at least three modes, normal, harvest and overtake, so how they want to make this work I don't know.
And of course they are just p!ssed off with racing point and mercedes...
PS. I am a composite engineer, so feel free to shoot holes in the above