I'll quote this because i really don't think my position on that is comparable to what you're putting forward there. I don't even personally know if it's a good example of what you referred to, since it points to different interpretations of your message. To say that it's good for a character not to have them being trans be the central tenet of their character does not acquire these potentially transgender characters the certainty of them being so in the first place through subtle references and clues, those two premises hang onto different kinds of interpretations and expectations. The former seems to want the representation to be "i am transgender, but more importantly, here's why it's so hard to be a teacher with how little they pay us" and the latter goes for a kind of hyper detail oriented search for symbols of potential transness. They operate on different kinds of communication from the creator and, personally, don't work well together because we're putting the audience in a place where they are both looking for the clues, i.e. not sure, but trusted to also understand that their search will only reveal a character's transness in a story where their transness is not to be the defining message of that character. I don't think that counts as very positive representation, personally.
I honestly got the feeling that Madeline was non binary just from playing the vanilla game, through what i can only explain as some deep sense of relatability that i can't put to clearer words because it's been so long since i've played it. My question here would be was that not a good representation of a trans character even before we had these clues (that i will not question or defend since that is not the point here), or, perhaps more specifically, of transness or the experience of being non binary? If the answer here is yes (which i tendentiously think it is), then these sorts of clues are pretty unnecessary, don't you think? However, if that's not the case, then these sorts of clues are a midway concession that aren't fruitful and only lead to the audience halfway being in on it and halfway standing on intuited ground.
That said, from a realistic and pragmatic point of view, i think it's more likely that the developer wanted to include some trans visibility in their game, maybe since they were more comfortable doing it at that point, and since the nature of development might have prohibited some bigger investment in letting us know through other more time/dev expensive ways, adding some suggestive assets was a high return low investment way of including it. Which, thinking about it now, is probably more of an indication of Madeline being "word of god" a trans/non-binary character than those screen shots. Because, honestly, short hair on little girls is an extremely common way of signifying some counter gender behaviour and i would not personally that as a little boy, but more as a little girl who had short hair who in my own head fit into the non gender conforming Madeline i already saw her as, but little more.