The amount of difference the brake size makes is lost in the noise of the factors that we don't try to control - budget, tires, driver skill, and a dozen other major variables.
Budget, tires and driver skill are all irrelevant factors.
Budget = when setting weights, prep always is assumed to be 100%.
Tires = when setting weights, prep always is assumed to be 100%.
Driver skill = when setting weights, maximum performance out of the car always is assumed.
Unless we have a dependent measure that isolates it, there's no way to know if the multiplier/adder/subtractor/whatever is "right."
You mean like the mid-engine adder? The FWD adder? The DW adder? Y'all built RWD versions of the classified FWD cars and did statistical testing under identical conditions? Same for cars with DWs? You moved the engine of an MR2 to the front to see what happens?
You are arguing that because we can not achieve perfection, we should not strive towards betterment. We've already got a situation where the weights are not "right" because we've ignored those factors.
Other ignored factors do impact the theoretical best lap time of the vehicle, but you are suggesting the cumulative errors of the ignored factors net to zero. That's not the case.
These things are going to need to be considered if IT gets to go to the big show, because if they aren't, people will look for the "unfair advantage" created by the gaps in weight classification (and lots of people will throw gobs of money at building 100% prepped versions of those cars) and all of IT will start looking like ITA -- one car to rule them all, one car to beat them.
Lap times are NOT that measure. We will NEVER know what lap time any car is truly capable of.
You'll note that I've spoken of theoretical lap times. But I will guarantee you if 10mm larger brakes is a positive factor, then, when prepped identically (per the process) and driven by identically skilled drivers (per the implication of the process), the car with the bigger brakes will beat the other car more often. That's simply the way the math works.