This is the thing with "protocol" ... and one of the reasons I puke in my mouth a little when OPS' in AA (or any minor league stats really) are cited to talk about a kid (as tempting as it is).
The team has an org plan with a kid - we want to see you do blah blah blah ... and if that happens, yay they are onto the next thing. It might show in the numbers, it might not. Now it sucks in an internet forum to have this be a black box - what fun is that? - but there you go.
With Benintendi, perhaps the targets are different - they wanted to see if his approach went to seed, if he could keep constructing good at-bats. Maybe the OF thing had a low score on their Benintendi-O-Meter because they simply assumed he'd be fine (if a born CF can't play LF then what are we doing with our lives).
I reckon Moncada was a slower roll for those sorts of reasons - maybe they wanted to see more craft at the plate (they weren't ignoring those wheelbarrows of Ks). The protocol is probably being followed, but the plan for every big prospect is its own snowflake.
The plan for hitting is less obvious than for pitching of course - no innings limits to worry about etc.