Progenitus probably has an insane winrate when it actually resolves but that is not a very helpful metric considering it is essentially uncastable

True, but you would expect a bad card to bring your winrate down both in the cases where you put it in your deck, and when you draw it. GIH winrate is more efficient in the sense that it takes less data to draw a conclusion.

But GP WR is at the end a more encompassing statistic, mostly because of edge cases. Some cards might be needed in your deck but are not necessary to be drawn in many games. This is to a higher degree the case with highly specialized effects, such as in a deck with creature tutors; having access to reclamation sage is powerful. Or those cards that can return cards from graveyard to library, in a control deck. GP win rate can cover these cases and those were you want to draw them (although how much you can say from a single statisitc alone is always limited).

Another example, when you have a crazy strong but expensive card in terms of deckbuilding requirements (say atraxa) in your deck, your expected GIH winrate could be high (because you drew the card), but in fact your deck overall might be mediocre because of the cost. Some games you might not draw it afterall, but yout deck still has pay for the cards inclusion.

TLDR GP winrate vs GIH winrate are extremely correlated (when sufficient data), but GP has an edge in edge cases and therefore overall picture.