I'm assuming that by "no direct before and after comparisions" you are talking about a blind test on 2 indentical GEN2 FJRs, one with the middle bushing and one without. That probably is not going to happen and I will admit that when I say I think the GEN2 forks handle and ride better than the GEN1s, I can't say for certain that the middle bushing is the only thing that is different between the forks.
The test need not be blind, though if it were that would add some credibility to the perceptions.
I guess I was thinking more of a before and after test on the same bike (to remove any other bike to bike variability) where someone removed the middle bushing and saw an improvement in compliance or loss of stability after the change. The fly in the ointment is that, usually when we are inside the forks we are also making other changes (improvements) to the forks, such as new bushings and oil at least. That would taint the results.
In regard to the effectiveness of a fork brace, I have not ridden a FJR with a fork brace but have not experienced any improvements on other bikes with fork braces, at least not on those that have been built in the last 20 years. However, if the tube walls on a GEN2 are thicker than those on a GEN1, I think that might explain why fork braces seem to be more effective on GEN1s,
I see claims for improvements in motorcycle handling with to the use of a fork brace that just do not make much sense to me. People like to hold the wheel between their knees and lever on the handlebars and say, "See! The brace stiffens the wheel from turning laterally", but realistically, how much are we actually levering on the handlebars? I don't even grip the bars very tightly when riding, so how important is it to hold the wheel perfectly perpendicular to the bars? And what road forces are trying to deflect the wheel laterally that we need to stiffen against? What exactly, from a mechanical sense, are the braces supposed to be accomplishing? I've never felt a need for increased precision in pointing the front wheel.
Any fork brace can do only one thing, and that is to clamp the two lower fork tubes so that they remain parallel to each other. It will not magically stiffen the (much longer and thinner) upper fork tubes, so they will still flex around the same amount as you ride over bumps.
I really can't see how the middle bushing would have any impact on the effectiveness of a fork brace. There are negatives to a fork brace besides the additional weight. A standard 3 piece fork brace can cause additional stiction unless it happens to be a perfect fit....which probably doesn't happen that often.
I suspect that you are right and that variability may explain some of the difference in perceptions about using braces. Even if the brace is manufactured to exacting tolerances, the outside of the fork tubes and their relationship to each other are probably not as precise, meaning the brace would fit differently on various examples of the same model bike. Any brace that forces the lower fork tubes into a position not naturally aligning with the uppers will increase the friction and add stiction.
Of course, there are also wide variations in how people
perceive almost anything in life, and motorcycle handling is certainly no different in that regard.