The shifting issue is partly me... I also own a '16 KTM 690 Enduro R, more on that later.
I've found that the R1 actually shifts pretty decent if shifted quickly, and just a little nudge one the shifter. Problem is, if I shift the KTM like that, I'll get a false neutral in 4-5-6 pretty consistently, so I shift slower and more deliberate. If I shift the R1 like the KTM, it clunks. Otherwise, the KTM shifts are buttery smooth, and I'm running amsoil dirt bike 10w60. Will do a UOA on that next year.