Puresummer why are you dragging this discussion back to toilets? I am so fucking bored of discussing toilets. There are many many non-toilet situations where the exceptions in the EA could be invoked but where instead women are kind enough to admit transwomen who they know and trust on an individual basis, or admit transwomen generally as long as they seem OK, on the understanding they can assert their right to female only space, should the piss be taken.
But as we are on the topic, yes we did used to have an honour system that worked very well in toilets for about 40 years, possibly longer. Now the transactivists have fucked that up by demanding as a right what was only ever offered as a favour. The result is that women are becoming increasingly mistrustful of any male person in female-only space no matter how feminine their attire or behaviour.
So yes, it has become tremendously legally risky for any woman to challenge the presence of any male person in any female-only space. As a direct result of this the trust has gone and this is no longer an honour system but an imposed law which harms women and girls.
Yay progress 
We can't look at self-ID in isolation because of the way the GRA interacts with the EA. Here are two paragraphs from the same page of recommendations in the trans equality report:
7.Within the current Parliament, the Government must bring forward proposals to update the Gender Recognition Act, in line with the principles of gender self-declaration that have been developed in other jurisdictions. In place of the present medicalised, quasi-judicial application process, an administrative process must be developed, centred on the wishes of the individual applicant, rather than on intensive analysis by doctors and lawyers. (Paragraph 45)
22.We recommend that the Equality Act be amended so that the occupational requirements provision and / or the single-sex / separate services provision shall not apply in relation to discrimination against a person whose acquired gender has been recognised under the Gender Recognition Act 2004. (Paragraph 132)
It is vital that we keep the exceptions in the EA that permit women and girls to have female-only space and it is vital that orgs can reliably use them without fear of litigation. The alternative is that the two recommendations above spell the end of sex-segregated spaces altogether.