I consider it more like pointing out that since the old rules are in service of a "polite fiction", possibly that is not worth having a practice of challenging anyone.
If the idea is to keep people out that don't look like the right sex, what about someone who looks in-between, and would not be well accepted in either restroom? If they are challenged, what should the owner or police do? So it seems to me even the "old rule" has scenarios not addressed, so now we are choosing what new rule to adopt.
If we try to avoid trouble by proposing a new strict rule that you must choose according to your birth gender, then we ask trans men to walk into the ladies' room possibly looking quite male. As well, someone ambiguous is either way still walking into a room with people that might find it uncomfortable, so in the end we have exactly the same problem we proposed to solve, only on top of that we have to figure out how to verify and enforce it.
So it seems to me there IS no rule that will keep people from seeing someone that makes them uncomfortable in a bathroom. In that case isn't it simpler to have no rule, and suggest people use whichever bathroom they find comfortable? And if an individual harasses another person, only then is it time to get owners or police involved. I feel like this is done successfully elsewhere without calamity. I also expect the lion's share of the time people will indeed select the restroom that matches how they present, at a rate we're not likely to exceed by piling on more rules than that.