Have you considered _ after using common sense safety _ putting your bike up on the center stand / starting it up / and at idle, put it into 1st or 2nd gear. Is the vibration that you describe present? You can judiciously add a little throttle /RPM.
You can see where I'm going with this ... maybe your suspension guy already did this isolation test.
Let us know...
I've done variations of this, and my suspension guy did the same. I know what you're getting at: putting on the center stand and adding RPM would isolate engine/transmission as source of the issue (or not).
But I'll do it again, and this time I'll turn the camera on the old iPhone I use as a navi, and record the results of this test. I'll also record the results of a ride, maybe this weekend. Won't be the same as a dedicated camera like Jess' but it will give a sense of the vibes I'm feeling when riding.
What I'd love is for someone to ride this bike o' mine, sans biases from this forum or my input, and come back with a yay or nay that there is anything besides a built-to-budget normal vibration. With more-or-less brand new Michelins, a very decent front suspension upgrade (which is noticeable, and not just placebo effect), and not much else done re: engine mods, this bike should be very docile and tractable. But it's fidgety in a way I don't remember for the first few years. It's been that way for nigh on a year now, and I've ridden less as a result.
I may take to one of our local reputable shops and have them just do the ride of which I speak and see if they feel anything. But that's a little ways down the road.