The Equality Act is not designed (despite its name), to ensure that all people are always treated equally.
It's designed to stop people (save for in justifiable contexts) from being treated unequally on certain, specified grounds (particularly those where there was been a long history of discrimination against classes of people, based on prejudice).
Honestly, how could you even have laws that simultaneously protect people from certain prejudices and also protect people's right to act, carte blanche, with the exact same type of prejudice?
(Yes, there are some cases where two protected characteristics will clash, and some sort of rights-balancing analysis is needed, but those should be - and are - fairly limited circumstances).