Well a randomised controlled trial would give the most accurate result, it's just not ethically possible for researchers to orchestrate this.
The best control would be a matched group who do not receive puberty suppressing treatment but were still trans identified, because what you want to discover is the direct impact of puberty suppressants on IQ, and trans status may already impact IQ ( eg. Do young trans people miss more education than non-trans people due to bullying, mental health concerns...do these issues relating to trans status impact IQ already? ).
So therefore a control group who is not trans is not really appropriate and limits the conclusions that can be made.
Future research may be able to do an analysis along these lines, but it would have to be with groups that had formed prior to and independent of the researchers' study concern, as the researchers should obviously not be assigning people to the study conditions of treatment vs non-treatment.
It seems likely that they did not have this data available to analyse (eg. Maybe these specific measurements have not been taken in trans adolescent populations who have not received puberty suppressants)
In any event, it is a far superior research effort in terms of relevance to the trans population than the study on children experiencing precocious puberty.
What did you think of the data showing "their educational achievement was on average higher. In our study, 51.4% of the participants was higher educated compared to 35.5% in the general Dutch population of the age of 15–25 years"
So a higher percentage of the trans population receiving treatment was higher educated compared to the general Dutch population.