Because these are minimum wage service staff, trying to balance a million things, and defuse tricky situations.
Why does my bus driver let people on who make a bad excuse about having lost their bus pass? Because the bus driver (often female, usually men who try this) wants to avoid aggro, and needs to keep the bus moving. If I stand up and say "But I know that man and I know he doesn't have a bus pass", the driver is not going to thank me. It doesn't mean anyone thinks the man has a right to be on the bus.
A business might need to provide single sex loos. They should then do what's reasonable to make sure they are single sex. Like not having signs up suggesting that people can go "wherever they feel most comfortable". If patrons are clearly taking the piss or causing a threat, staff should intervene. It's not realistic for staff to take time out of their working day to somehow verify the biological sex of a trans man who has popped into the gents at their own risk and caused no trouble to anyone, so that you can prove a point. But go ahead, if you want to.