Cool discussion. We too are on an RT. I purchased the bypass a while back and replaced the oem primary muffler / cat whatever we deem it to be.
As a group, I would say it is safe to say the bypass alone does work well and improve performance over stock.
The F3 and the RT may have the same basic engine, same basic exhaust but differ in the final muffler itself. This may or may not make a difference.
It is well accepted that for high rpm use on most vehicles, and exhaust with no baffling at all tends to provide the greatest amount of HP in a smaller window of rpm range.
So, a straight thru system, on a Spyder, such as a Yosh, Two Brothers or similar may not be optimum for everyone.
A baffled muffler with a bypass pipe may provide enough restriction to work well for others.
As far as the baffles installed into any exhaust. Often they serve two purposes. One is sound reduction. The second could be power delivery. Most baffles are known to increase mid range torque, not so much HP, but the baffled exhaust often falls off in peak power and torque at higher rpms.
The non baffled exhaust could have less mid range torque than a baffled exhaust but could outperform the baffled version at high rpms.
Many people did not enjoy the "tone" of the bypassed exhaust and wanted a deeper less "ricer" sound to their Spyder.
The baffle not only provides less free flow to the exhaust, the real key is that the exhaust pulse wave is altered. In theory the exhaust pipe dimension from the exhaust valve to the restriction, (original primary muffler, the baffle in the muffler when running a bypass or the baffle inserted into the bypass) all have a given length. The length of the pipe from valve to restriction tunes the resonance in the entire exhaust. If the length is short, it typically but not always reduces torque, if the length is longer it typically increases torque.
There are other factors, such as the effect of the cooling of exhaust gases causes them to slow and creates a restriction. A change in the pipes cross sectional area also changes the way the flow moves through the pipe.
In summary, I do not run the baffle. I immediately realized the power delivery changed with the bypass and improved once the computer optimized the the F/A ratio. I do find that over 6k rpm, and seldom do I turn the RTS that high, the power does "feel" like it goes flat.
Here's the kicker though, without seeing torque curves, from the same machine, running different exhaust configurations, and dynoe after the computer has had run time to optimize the settings, it truly is subjective to what the rider feels AND what rpm the rider tends to run the Spyder at.
I must also add, and this is based on tuning many race bikes for many years, very often, the rider hears what they think is fast. Not saying anyone posting is right or wrong, simply that from testing, and lap times, what the rider says is fast, sometimes is not correct and often the "sound" of fast is different for different people.
The really odd item in all of this, the dyno info that was shared by Pitbull / Lamonster seemed to indicate the 10% increase in power came from their in house exhaust system with I believe has a non baffle mid pipe, and straight thru muffler. The restriction is very close to the end of the muffler. If I am incorrect about this, please make the info about the Pitbull cat back exhaust correct.