I am referring to the reed valves that sit on the sides of the engine, that dump extra air into the exhaust during decel to burn off unburned fuel. I believe those operate using manifold vacuum. These are typically removed with an ear shave, and a plate is put in place where the reed valves used to sit. As I understand it, putting these plates in place stop the popping on decel.
When I did my ear shave last year, I left that system in place, because I like the popping on decel. I didn't notice any issues with the enriching diaphragms in my carb. It ran more or less the same as before the ear shave. Only more intake noise and slightly improved MPG. I did notice that running the idle screw slightly richer than optimal, got rid of the popping.
For the Tuxedo mod, I've got the cover off (needed to remove it anyways, to remove the cam chains). It will be modified off the bike, in a different building, in a different city and county /forum/images/VN750_2015/smilies/tango_face_grin.png. I actually didn't realize that people try to do this mod on bike. That doesn't sound like a good plan, for the reasons you outlined.
Yep, there’s a video on YouTube of some guy cutting the engine while on the bike. With a drummer like tool nonetheless. Even I a novice to mechanic work said “are you f—kin nuts?” When I saw this.