There are any number of issues with the article but I'll leave that to one side.
I actually watched the video he linked to and it was far from being transphobic. This was typical of the content:-
If you have met one transgender person, you have met one transgender person. No two experiences are the same.
Although, to be totally fair, some of the attitudes expressed were a bit 
- I'm not religious at all - but, leaving that aside, the advice they gave in the video I could totally get behind, for example:-
There are also practical steps we as churches must address. Providing toilets that are clearly accessible to trans people will be an important part of welcoming people into our churches or our charitable organisations. Placing a "Toilet Access For All" sign on an individual disabled toilet was considered helpful by a number of trans groups that we spoke with.
In relation to changing facilities and residentials; the best advice is to discuss the matter with those concerned. There is no single, simple recommended or legal solution.
There is significant scientific and medical disagreement in this area. An NHS publication on gender identity clinics notes that "There are currently no agreed measures of success or patient outcome measures. This makes determining good patient care ... very difficult"
[Note - this video dates from a couple of years ago - well before the Keira Bell case]. The video goes on to claim:-
There are some important trends that are worth knowing about. The first is that referral rates are up over 1,000% during the last six years, although that starts from a very low base so that statistic is slightly skewed.
The second is that the average age of referral has gone up and that is linked to the third, a shift from 58% of children born male attending the clinic to now it's almost 70% of children born female.
So, basically, it used to be younger boys who were going to the transgender clinic and now it's older teenage girls who are going and that is linked to this rise in rapid onset gender dysphoria where teenage girls are attending and they often know one another and there are fears about a social contagion effect.
And the fourth is that 80% of those children who attend Tavistock before adolescence are likely to eventually change their minds and revert to their birth sex. Conversely, for those who come during adolescence, the figures are reversed and about 80% pursue gender reassignment.
So, it used to be young boys who attended the clinic and they were less likely to go through with it, now it's older girls who are attending the clinic and they are more likely to pursue reassignment.
The video then goes on to explain about puberty blockers, cross sex hormones and surgery in an accurate and non-judgmental way although it does say that even the Tavistock admitted that it had no idea about the long term effects of such treatment.
Then there was a claim they made that I don't know where they got it from but I would want to follow it up as (although I do believe it is likely) it does sound as though it may be as robust as the trans suicide figures promoted by Mermaids et al are (in other words, not robust at all):-
And, sadly, while rates for attempting suicide for those who identify as trans are very high - 27% of trans young people compared with 11% of all young people - it should be noted that those who have had transition surgery are 19 times more likely to die by suicide than average. So transition is, sadly, rarely the answer.
The video then goes on about various legal issues which, quite presciently given that this was from 2018, covered things like consent and free speech.
I am not religious at all (quite the opposite of religious in fact) but the ending of the video made me stop and think that perhaps not all churches are as bad as I thought they were:-
Finally, what should the church's responses look like? The church must respond with compassion. The church can be [can be ?], and often is, a place of welcome for everyone, especially those who feel marginalised.
The journey to reconciliation between somebody's body and their experience of their identity can often be long and painful. We need to be prepared to offer them and their families long term support and care.
This does not negate the church's discipleship role, particularly among those engaged in the wider trans movement which is often at odds with the biblical response.
Secondly, the church must seek clarity in this difficult area. Whilst we seek to support those struggling with gender dysphoria we can resist and oppose forms of transgender ideology that offer alternative and radically non-Christian ideas about what it means to be human [I wonder if he means as in "adult female"].
The church must be careful to respond pastorally to individuals whilst recognising the challenges and complexities surrounding transgender.
And finally, the church should, with humility, give voice to some of its concerns. The church, like many others, is cautious about the rush to invasive and non-reversible medication and procedures - particularly in children. [again - this was from two years ago]
Many Christians will also sympathise with concerns being raised by womens groups and others about both the safety of women, for example in womens refuges, but more fundamentally about their very identity being challenged.
There is an ever present danger of being misheard in an increasingly divisive public conversation and so we must seek to build good relationships and ensure that we speak with grace and respect at all times.
OK, so they do actually go on a bit about God (well, hey, they are a church) but that video was not transphobic at all and, if anything, was a lot more respectful than some comments that appear on mumsnet from time to time.
Overall, I really do think that this Guardian columnist was looking for something to be offended about.