I have found that 9000/9070 front derailleurs have to be set up a little higher than before, erring towards the 3mm max height over the big ring. This is due to that little bump that hangs over the OP's wear area. When in the hardest cog in the big ring, the chain should pass just under the bump. Set up traditionally, it will rub a good portion of the time, probably in the 3 hardest cogs.
I have not had any customers with this complaint yet. Considering the OP's front derailleur still has the inner cage plastic guide with no appreciable wear, and the shift to the big ring is much more stressful than the downshift, it is clear that the chain has been rubbing, at least intermittently. Or there are squirrels running around with a taste for nickel plate.
Great observation and tip. I've had a tough time finding the right combination of adjustments to dial out a bit of rubbing in the gear combos you describe. I've always tried to go as low as possible with my FD positioning. As you mention, this may not be correct with the 9000. I'm going to try the higher position - thanks!