1. The principle of Accommodation
It might be uncomfortable to admit this but congregations are a mixed bunch. We are all a work in progress, putting sins to death and learning new things about God. I think it's helpful to distinguish between basic functional obedience (more on that below) and the permanent co-existence of different views on this side of eternity. If someone's foul language, violence or avarice is disruptive to the shared life of the congregation, then they can't participate. You simply can't accommodate people who refuse to allow the congregation to function. The larger society (including Christians) may have ways of helping them but the purpose of the congregation is to gather and collectively worship God and grow through discipleship.
Because we live in a world broken by sin (discipleship, discussed below, is focused more on dealing with the corruption of sin) we will gather with people who behave differently. We gather with disorganised, eccentric and hurting people. Additionally some have stricter or looser views about the participation of women, the use of instruments, the nature of the sacraments or the shape of sermons for example. Just as God accommodates himself to us, we accommodate ourselves to our brothers and sisters in Christ. Now within this, is of course a place for gently shifting someone else's patterns of behaviour or thoughts. The pastoral life of a church should be considered a permanent ongoing discussion of how best to follow Jesus.
So when it comes to people transitioning gender, we should be distinguishing between encouraging that transition (which is wrong) and being welcoming (which is right). For example if someone believes strange conspiracy theories but doesn't make a big deal of them with other people why shouldn't they be welcomed? We shouldn't encourage sin, but it may take a long time to work out how to have faith in all areas of your life. I think it's easier if someone hasn't made biological modifications to their body and more difficult if the transition is dramatic. For someone who has transitioned genders past the point of no return, they should be met half-way. What does this look like? For example: the congregation using new personal pronouns, the transgender person remaining celibate and (safely) conceding their sin, permanently etched into their body.
2. Active Discipleship
Which brings us to second principle: discipleship. From the beginning the new covenant communities have been shaped by catechism and spiritual discipleship. (For example I've illustrated this post with a picture of the Didache, one of our earliest Christian documents.) With the marginalisation of Christianity in the 21st century we've entered a healthy time of focus. Rory Shiner observes this in his article about the new shape of Christian congregations. Discipleship is a life-long project that begins with evangelism and then, as someone trusts Jesus and grows in their faith extends through out their life on this side of eternity.
Discipleship is the basic work of the church, the local gatherings of God's people. We then grow the Kingdom by applying our faith to the rest of our lives. Discipleship is the bread and butter of Christian ministry, it's about communicating the essence of the gospel and then a deepening knowledge of God and theology. Practically discipleship includes things like participating in the gathered life of the church, one to one Bible reading, training, small discussion groups and para-church events. Notably, discipleship occurs within the larger sphere of Pastoral Care, which seeks to strengthen the well being the congregation.
So hopefully someone who had been transitioning genders and who now trusts Jesus is in the midst of active discipleship. Growing in their knowledge of God. Just as the principle of accommodation requires deep reservoirs of calmness, generosity and patience, active discipleship requires a focus of resources and priorities. Church is no longer a magical attraction machine, but a safe place with high entry requirements. Theoretically, emphasizing the safety of the gathering should guard against the legalism of a 'holy huddle' and the focus on discipleship should encourage people let their faith filter across their fence, desk or shop counter. Basically the goal is for everyone to be loving Jesus more than their sin.
[Fragment of the Didache]