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HR/Fly is HR/OUTFIELD Fly...not HR/total fly. Historically, the HR/OUTFIELD fly is 11%. This year, the HR/OUTFIELD Fly is also close to 11%. Take the pop-ups out of your flyball numbers and you'll see it.
The HR/FLy that's listed at Fangraphs is also HR/OUTFIELD fly (FB - IFFB).