Small, it may be this . . . .
. . . I got in some more riding in the last two days and was finally able to create ( maybe ) your vibration.
In my last tests, I moved through the 60-90 MPH range and could not detect anything like a vibration. For about 20 miles, I tried that in both 5th & 6th gears, slowly throttling up and down to see if I could find any area of 'vibration'. Nope. I checked my belt as well as I could and it was at spec.
Yesterday and today I was out again - @ 250 miles, I am still in break-in mode, but testing some limits - and maybe I ran across what you are experiencing.
In 5th & 6th gear - going over 50mph, if I 'cranked' the throttle ( like to quickly pass or to put more space behind me from an approaching vehicle ) the engine would roar to life and the F3 would shoot ahead. There was a 'vibration', but it was ( to me ) just the engine/exhaust roaring to life. It only lasts a second. It didn't feel like "grinding" or anything bad. There was no hesitation in how the power-curve felt or that the belt or transmission was slipping.
Really, it felt like if you are sitting on the F3, with your feet firmly planted on the pegs, and start it up. To me, it does this va-Rooom thing - where the "R" in the "Room" part is accented and the "oom" part is a descending growl. I get the same 'vibration' on my F3 at startup, it is just not as strong as it is at 70mph.
Actually, you can kind of see/hear what I am talking about if you look at the video Lamont posted where the Spyder is started up and rev'd a couple times without a muffler.
That ":cus:-off" tearing/shredding exhaust sounds like the 'vibration' feels.
So, to recap:
No "vibration or grinding" when doing an easy roll of the throttle while in 5th or 6th gear at any speed between 50mph & 90mph.
Vibration/sensation when fast acceleration in 5th or 6th gear between 50mph 70mph. Nothing noted in downshifting or deceleration in that speed/gear range.
Lower intensity vibration/sensation at startup, when motor comes to life. ( no belt involved )
No, it is not your imagination. ( BRP may call it a feature. )
My Spyder GS or ST-S, never did anything quite like this - but as much fun as they were, they never performed like an F3 either.
If what I did and felt matches the conditions you were in when you felt it, I don't think it is a problem. A different muffler may tame it down or perhaps make it more noticeable. I would be interested if a belt-tensioner would change anything, so, like you, I will keep my eyes and ears open. I am no Scotty and I only have my years of motorcycling/car experience to go by - but I am not concerned.
As always, consider advice, but make up your own mind.
Tom