I don't understand why you'd jump to the assumption that they didn't factor in such an obvious thing, especially since the researcher already lists possible explanations for the discrepency in the article:
“We do not know why more individuals from deprived areas had a transgender code in their records, and if this really means that there are more transgender people in those areas, or if they are simply more likely to be recorded as such in the NHS GP [general practitioner] records. Transgender people face stigma and discrimination in society, potentially leading to exclusion from employment, education and family support, which might make them more likely to move to deprived areas. Some areas might also be more ‘trans friendly’ than others. Another possibility is that transgender people in affluent areas were more likely to access specialist gender care privately, bypassing their GP and the long NHS gender clinic waiting list entirely.”