Returning to the OP's question about genuine gender dysphoria (so setting aside cases where AGP or abusive behaviour is at play), I think the church response depends very much on what the claim is for what genuine gender dysphoria actually is. And that is where the real difficulty is, because it seems incredibly hard to pin down and articulate it in a generalisable way that doesn't rely on reaching for Gnostic concepts.
I think there are two ways you can jump on that observation. One is that the mutability and lack of precision in claims about what gender and gender dysphoria are means that we should be sceptical about treating them as a stable, objective concept. The second admits of the possibility that there are people with 'real' dysphoria who are using the Gnostic framing because they've learned that that is the language which our culture responds to.
So say that there is 'real dysphoria' - we first need to be clear about what this is, and then formulate a response to it, including whether transition, from a Christian pov, is something the church should support and, crucially, what we actually mean by it if we "affirm".
Assuming you reject the Gnostic conceptualisation of gender identity (which I have to say I do think we should just straightforwardly reject as Christians) then the best candidate for 'real dysphoria' is probably something like 'a deep and permanent sense of discomfort with one's sexed body'. The question then is what the right pastoral response is to that.
Any pastoral response, it seems to me, has to acknowledge that there are natural hard limits to how fully the church can embrace transition - i.e. it can't mean an uncritical acceptance of the idea that someone is "really" the other sex. Firstly, there's a hard limit on baptism. Trans people have sometimes wanted a second baptism in their new name. We should be unequivocal that baptism is a one-time thing. Secondly there should be (in my view) a hard limit on affirming transition in contexts where sex matters, like parish safeguarding - it should never be the case that we don't recognise sex for safeguarding purposes. Thirdly, where transition is implicated in the breakdown of a marriage or the break-up of family relationships, we need to be clear that this is a grave matter, that the non-trans spouse or family have clear pastoral needs too, and that straighforwardly affirming transition may not be the right pastoral response as far as they are concerned. Fourthly, we should be clear that creation is good, and that there are no 'wrong bodies'.
Then there's a set of wider pastoral issues that are less clear cut but which need considered responses, like what do you say to congregants who think that transition is a form of lying, how do you run single sex social or study groups, how do you present transition to children in the congregation, and how do you deal with AGP and men who want to gatecrash women's spaces if you are affirming some people but not others.
So can the church be inclusive on transition? I think my answer is, possibly, in some circumstances, yes, but it needs very strong pastoral leadership, clear articulation of where the limits of affirming transition are, a lot of emotional and spiritual maturity on the part of the trans person and the rest of the congregation, and a clear conviction that the costs of doing it are not too high to bear. And in all this there is the question of should: we may need to weigh whether we are truly acting in the best interests of the trans person by affirming, rather than supporting them to accept the truth about their body or live with the discomfort in the way we ask other people to make sacrifices as part of following Christ.
A very imperfect analogy here is that a church I used to attend got into trouble with the bishop for using only alcohol-free wine at communion (this was not in the CofE). This was an inclusion measure, so that a small number of alcoholics who were in the congregation and wanted to be completely abstinent didn't feel reminded of that every time they took communion. The bishop came down very hard on this and made it clear that inclusion couldn't come at the cost of putting aside canon law, which says that you need to use real wine. So we had to accept that we couldn't have perfect inclusion in the way we wanted to, and the individuals affected had to accept they couldn't take communion in both kinds, and had to live with the reminder of that.