At one point, she told the court that she would "respect" trans people, but defended her right to misgender them. Which is why the Employment Judge made the comments about how this judgement does NOT give her that right.
I think this potentially creates a problem. The lower tribunal judge found that it was not that her GC beliefs were problematic, gender critical beliefs would almost certainly be protected, but that it was inherent in her beliefs that she had the right to misgender someone or ignore a gender recognition certificate when she thinks it's appropriate, such as if a trans person uses single sex spaces - which could mean calling a trans woman a man every time they went to the toilet. Today's judgement took her claim that she respected the human rights of trans people and that she would normally use preferred pronouns at face value which given her more recent output on twitter and that of her supporters seems a bit naive. It also seems to suggest she has the (protected) right to believe she can misgender people in the workplace whenever she deems appropriate, but if she actually does that it may constitute harassment. That seems a bit of a mess to me - it is likely to result in some people thinking they can treat trans people however they want at work and it creates a problem for HR departments to really know what is and isn't likely to be lawful.