On the '15+ R1, remember that there are two different functions I think Jim is bringing up.
Linked brakes: Using the front and/or rear control activates different percentages of each. Meaning your front brake lever may actually generate rear brake pressure (at a lower pressure) along with front brake pressure (at a higher pressure).
ABS: The R1 uses the combination of front and rear wheel sensors combined with the accelerometer to modulate the brake pressure - whether it be front or rear brake pressure.
To my knowledge complete elimination of the ABS module (usually combined with something like the FTECU ABS disable plug) and replacement of the brake lines completely eliminates both. Also to be clear, factory riders are required to lose them at least for Superstock/supersport I believe. ABS is legal for Superbike only if it is exactly as delivered OEM (for MotoAmerica). Many car racing organizations prohibit it. Not because it doesn't work - but because it can give a technical advantage so it's prohibited. F1 for example requires "manual control" of brakes. Modern performance oriented ABS over the past few years has proven to be extraordinarily capable - testing at the N'Ring, etc shows that a "good" ABS system lowered lap times with professional drivers.
I'm running my ABS until I feel as though it's getting in my way. Too early to tell. My theory is that guys like Elias or Gerloff may have far better "feel" for the limits of the tires, so they may not want artificial feedback. I may never be as good with that feel as the ABS algorithm, so it's just possible that ABS may keep me off of the ground. Or, it could diminish threshold braking and I could end up running off. Lenny is racing with ABS on his R1. Jim is right in that particularly at our level, it's probably a personal feeling.