We aren't disagreeing about that.
What I'm saying is that, as with any rule that a business must ask their customers to follow, there is no magic wand.
You've brought up an imagined edge case, in which it's not clear to staff that a rule has even been broken (it's just your say-so). What do you honestly expect to happen? I can't tell you, because I can't speak for every public-facing service sector employee in the land. If I were the employee and you came to me with that tale, I'd be thinking "Oh JFC, WTAF. Why do we live in upside-down world, and why can't this guy just wait a moment to use the loos". Then maybe I'd ask a male colleague to pop his head round the door.
Ultimately, the service provider has to judge the consequences. If they are advertising that anyone can go anywhere, or consistently refusing to deal with obvious breaches, then they're clearly taking a big risk with the law. If they're letting predatory men stalk about in the ladies' changing rooms with their cocks out, then they are taking risks with public safety too - and they can now be confident in dealing with any such incidents, no longer paralysed by the notion that the Equality Act forbids them to. If a man rushes up to the Reception desk effectively saying "there's a lady in the gents, she looks like a man but I went to school with her and I know she's not", the staff are going to have to weigh up WTF is truly going on here, who the troublemaker is, who is actually at risk, and what a reasonable response is, by which time said lady has probably left the gents and moved on.
I can see why you've invented this scenario, because it's the mirror image of what transactivists have always liked to imagine - the mythical trans woman who passes, and the mythical Karens who somehow find out and have the vulnerable trans woman forcibly removed pending "genital inspection". Funnily enough I've never witnessed that - only cross-dressers parading about for hours in the loos as if marking out territory, while women try to get in and out as quickly as they can, or avoid the facilities entirely. I've also never once, ever, heard of men coming to harm, being filmed, etc by a woman in male or mixed facilities.
By all means, if you are troubled by a transman in the gents at any time, go and complain. I don't disagree. Meanwhile, I will write to my bus company complaining that it's not fair to let fare-dodgers stay on the bus. We are both righteous crusaders. I'll save most of my crusading energy on protecting women and girls, though.