You might think that this
" For example, a lack of inquiry means we have no accurate data or high quality evidence on whether gender diverse people are more or less affected by covid-19, and thus whether public health and medical advice ought to be different for trans people taking cross-sex hormones."
would mean that people on such hormones would actively want to stand up and be counted accurately, so that their medical care might be improved.
In fact, I would have thought that making sure you were transgender would be something anyone transgender would want to be counted as being in the census, because the more of them there are the more they will get the treatments they need in the NHS -- but it seems many don't see it that way.