I've seen that too, but I wasn't sure how to tell if a vibe is caused by unsynced throttle bodies or not and the procedure to sync them looked pretty in depth. If my motor mounts are torqued good and there are no loose throttle body boot clamps then I might need to try a sync.
Just to give you a little background on this issue, many riders are complaining of viby bikes from Gen2 (2012) forward (do a search). It seems to impact a small fraction of the new bikes and there does not seem to be a definitive cause nor fix. The dealers will not fix this and claim that it is "normal" when it clearly is not. Crash bars and side-case brackets do not cause the vibration but just make it more noticeable. The "throttle body sync" in the Suzuki manual is for the idle-air circuit only which cannot cause motor imbalance and only impacts idle and just-off-idle (<2000 RPM) whereas the vibes are typically in the 4-5000 RPM range indicating motor imbalance. There used to be a procedure in the Suzuki manual to sync the primary butterfly valves in the throttle body but for 2007 and later models that procedure was pulled and the manual says never to touch the throttle body linkage adjustment screws so the dealer will never do this. The Rx in the manual for out-of-sync butterfly valves is to completely replace the throttle body at $800 which is why the dealers won't do that under warranty on just a hunch.
Here is a brief history of my experience with a 2014 Wee that I bought used with only 3000 miles on it. The bike was viby from the day I bought it and the seller admitted that it came that way from the factory. He was an ex-Harley rider and thought it was normal, lol. The vibration was so bad that I was considering selling it. The crash bars would buzz like a hive of angry bees and I could feel vibes in the seat, pegs, bars and the mirrors were useless at speed.
The primary cause was the loose lower throttle body clamp that I mentioned in post #2 that probably came that way from the factory. I also found that the secondary butterflies where noticeably out-out-of synch and just used calipers to adjust them. The secondaries are not critical to motor balance so they don't need high-precision. Fixing the boot clamp and the secondaries got the vibs down significantly.
I also re-positioned the motor in its craddle and retorqued the bolts which lowered the vibration further and made the mirrors useable at speed. I also removed the crash bars but can still feel vibs in the seat, pegs and bars but at least it is tolerable for now. I don't think that the secondary butterflies came from the factory out of whack so I suspect that the seller also messed with the primary linkage trying to get the vibes down and that is the source of my problem now.
My previous bike was a K7 Wee and it had an idle-hunt problem and was viby.
I figured out a way to rebuild the throttle body and developed a procedure to balance the primary butterflies using LED light. The problem with that bike with 80K miles was the shaft seals were worn and leaking so I replaced the throttle bodies with used ones that I used my sync procedure on and that bike was as smooth as silk all the way to red-line. Eventually I will probably dust off this procedure and resycn the throttle bodies on my L4 but it is a complicated procedure that I am hoping to avoid.
Before I proceed with that plan I have since measured the compression twice with two different compression gauges and got mixed results. One showed a F/R delta of 20 PSI (spec in manual is 28 PSI) which would explain motor imbalance, possible due to running the front cylinder lean for 4000 miles before I found the loose throttle body boot clamp. The second test showed F/R 0 PSI delta (i.e. normal) so before I pursue that avenue I am going to rerun the compression check again and may do a leakdown test. In thinking about this more generally, I thought that one of the only major changes from Gen1 to Gen2+ (assuming the Gladius motor is not inherently viby) is that exhaust was redesigned so I am also looking to modify/adjust the exhaust mounts to see if that can be a cause.
But the question, for you anyway, is what could cause a brand new bike from the factory to be so viby? After ruling out vacuum leaks or compression delta between cyclinders or motor mounts, I think it has to be either the exhaust mounts or an out-of-synch throttle body. The throttle body synch of the primary butterflies is a high precision adjustment and is probably done by Mikuni on special machines that are recalibrated after so many hours or X number of throttle bodies synched. If you happen to get a throttle body synched just before calibration, you get a viby bike. If you get a bike with a throttle body syched soon after calibration you get a smooth bike. Luck of the draw.
My case is different than yours because the seller may have messed with the throttle bodies but if I do my high-precision synch and my vibes go away (after ruling out other causes) then this could explain the small fraction of new bikes coming viby from the factory.
