My take on Adler's cross-dressing was always based on the operatic connections, because that was incredibly common and would have meant that it would have less significance to her, potentially, than a woman not brought up in the theater. By which I mean the transgression was there, but it seems likely to me that she felt it less because it was more common in her world than most women.

One thought I just had, and forgive me for not having it thoroughly thought-out, is that it's possible that Doyle put her in men's clothes because to make her an appropriate "rival" for Holmes she had to taken to some extent the power of a man. For her to be worthy of defeating him, she cannot move merely in women's circles. It's possible that it indicates not only her rebellion--and I'm not sure how Doyle would have thought about that--but his need for her to literally wear the pants.