The difference is that everyone knows that non trans men enter nightclub bathrooms and rape women. That isn't news to people. The majority of the population know it's happening and that it's wrong.
Whereas huge numbers of people are only just finding out about transwomen in women's prisons, in sport etc and what that means for women. That's why it's such a huge topic at the moment, because new people are finding out just how much of an issue it is all the time and starting conversations like this one.
And the trans issue affects the other issues too. Until the last 10 years, if a man tried entering a women's toilet in a nightclub, upon being spotted they'd have been hoiked out of there, ejected from the club (and probably been given a kicking) by the bouncers and potentially been arrested. Obviously it's not 100% effective, but there's a social contract in place that stated that a man trying to enter a women's single sex space will be treated with suspicion and hostility.
That social contract is now gone. Is that man actually a trans woman? They've likely still got a penis, but that means nothing now. Hell even a beard isn't a reliable indicator. If I call this bloke out then am I going to be fired from my job?
It holds true for all areas of feminism. Women not getting recognised in the workplace, well now we've got men on all women shortlists, women's categories of awards being removed.
It's insidious, it's not a small issue, and it affects every area where being a woman is already shit.