To a certain extent we have a philosophical topic here. It is one thing to ask, "What did a player accomplish in 2017" and a different thing to ask "what do we think a player's 2017 component-skills record predicts he will do in 2018." James is emphasizing the former; Fangraphs is emphasizing the latter -- to the point where 2018's projection becomes, de facto, their historical record of what he did in 2017.
Take xFIP, for example. Fangraphs can and will argue Cy Young based on xFIP, whether or not a pitcher actually threw a bunch of poorly-located gopher balls that created a large ERA-xFIP. They can, and will, assume that any variation between 11% and a pitcher's actual HR/F was nonsense and should be discarded.
James is merely arguing that if a pitcher gave up 7%, or 14%, homers per fly then that is the history of the matter. I would add that there are times, a minority of times, in which that HR/F rate was skill-based (over the course of a season or two) and that GM's certainly will consider that.
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Could go line-by-line on the rest of it but of course you are right, in terms of the point you are making CPB. Thanks.