As far as I understand, the max fuel flow rate of 100kg/hr was put in place to limit the engine power. For a given fuel flow, you can only extract so much energy, so by imposing a max fuel flow rate you impose a limit on the amount of power that can be generated by the power unit.
I think the intention here was to stop teams spending money on developing power units with crazy qualifying modes - I'm thinking of the rumoured 1500+hp qualifying engines of the 80s.
For PU manufacturers, the fuel flow limit rewards those that have the most efficient PUs, which aligns with their commercial aims. Also by having a fuel flow limit, different engines will converge over time in their maximum power output as they approach the theoretical efficiency limits of hybrid power units (somewhere around 50%).
What I don't understand is why we have the fuel allowance for a race (currently 110kg, up from 105kg last year). Every kg of fuel that a car starts with in the race is a weight penalty. A team will calculate the amount of fuel they will need to give the fastest time to the flag. This may include some lift-and-coast fuel saving on some tracks, depending on the fuel consumption - and we know many teams short-fill their cars based on this calculation.
But my point is that the amount of fuel is self limiting. No team is going to carry more fuel than they calculate is the optimal amount so why mandate a maximum?