Saying it's a direct A/B comparison is seriously overstating it. Transitioning is itself a huge confounder, and if it were true that time before/after were exactly comparable, that would debunk one of the main justifications for allowing sex-changes in the first place!

Also, confirmation bias on the subjects (if you assume that workplace sexism is a thing, then you are probably more likely to notice people doubting your competence and register it as "sexism" when you are a woman rather than when you are a man), confirmation bias/publication bias on the authors of these "studies" (would a book about how trans-people experience no changes in workplace interactions get published? Would it get a review on New Republic?), smal sample, likely sampling bias (how were the subjects selected?), no attempts to falsify the hypothesis, and in general all the ills of arguing from anecdotal evidence.