It refers to someone one who is ‘a woman and not a transsexual person’. The comparator would be a woman who IS a transsexual person.’ Would you suggest that a trans man - who is a biological female - would be acceptable? That is what this guidance excludes - a man who is a transsexual person.
Let's look at the actual wording in the EA.
A counsellor working with victims of rape might have to be a woman and not a transsexual person, even if she has a Gender Recognition Certificate, in order to avoid causing them further distress.
Do you really think they are talking about a transman here? It says "Even if she has a GRC". Why would they refer to a transman with a GRC as 'she'? And why 'even' if she has a GRC? A transman having a GRC would make them less eligible for a female-only position than a transman without, since they would have become a man in legal terms, and should be treated (in most cases) as a man.
If you read through other instances of where they refer to transsexual people, they always use 'she' for MtF and 'he' for FtM, so this also makes it unlikely that it is a transman who is being referred to here.
The EA2010 also gives this example in the explanatory notes (para 740):
A group counselling session is provided for female victims of sexual assault. The organisers do not allow transsexual people to attend as they judge that the clients who attend the group session are unlikely to do so if a male-to-female transsexual person was also there. This would be lawful.
www.legislation.gov.uk/ukpga/2010/15/notes/division/3/16/20/7/5
It's quite clear who they are talking about here.