I haven't done any research on how the FJR linked brakes work, so I can't really speak about them. However, having ridden my FJR for a few weeks now, I can tell you that because the rear brake is actuated when I use the front brakes (to a degree), I have yet to actually use my rear brake for anything other than holding the bike still at an intersection. I will say that even that amount of use is limited; since old habits die hard, I rarely take my hands off the controls at stop lights - I tend to leave the bike in gear so I can make a quick exit if I see or hear skidding cars anywhere nearby. I did tend to drag the rear brake during track days when heading into highs speed corners, but that was to avoid upsetting the suspension at high speed, but that's a different topic.
I can say that there is no way activating only the rear brake on a linked braking system will give you the proper amount of front brake to effectively stop the bike in an emergency situation... even with ABS. My opinion is that w/ linked brakes if you are going to ignore one brake, you're better off not using the rear vs. the front. Folks get weirded out about locking up a front wheel and while it can be disastrous, ABS will prevent the front from locking up. I was trained on an old Kawasaki KZ1000 w/ no ABS and crap tires. It still took quite a bit to lock up the front, however the rear locked up in an instant which made it useless and hard to control.
From my experience I can tell you that the tested cone patterns that we taught are a quite a bit easier when you can drag the rear brake through the pattern. Part of the "no brake" reasoning is to teach complete clutch/throttle control to regulate speed. When utilized properly, the rider is pretty much slipping the clutch during the entire pattern. Rarely is the clutch fully engaged. I would imagine that a class that teaches the use of rear brake is only teaching to "drag" the brake which probably puts very little braking to the front which makes it negligible. If a rider in those patterns "stabs" the rear brake in panic, then they are going to fall down or put a foot down. The key is not to panic and use the clutch/throttle to power out of the pattern and try again. Dragging the rear brake offers resistance that can give the rider confidence, I'd liken it to cornering going uphill vs. downhill - most people will say they feel better going up vs. down.