This was a decision of the County Court - the lowest civil court - and as such it does not make legal precedent.
It's impossible to know the full detail of the court's decision because County Court decisions are not reported like those of the higher courts.
However from the summary the court has not said that it is "not true" that toilets are protected by sex not gender.
There is no protected characteristic of gender in equality legislation.
The two relevant PCs are sex and gender reassignment.
The Equality Act says that services may be provided separately or differently for people of each sex, and that it is not sex discrimination provided that is "a proportionate means of achieving a legitimate aim."
There is no obligation under equality legislation for organisations to provide single sex toilets (or any kind of toilets for that matter). The law means that when they do they are allowed to provide separate toilets for people of each sex and this is not sex discrimination.
What I get from the outline of the court's judgment is that this transwoman was treated quite badly by the landlord even after she was asked not to use the ladies toilets, to the extent that she won her claim of harassment. Whatever ones views on transwomen accessing women only facilities, I think we all agree that transwomen should not be harassed or abused.