EHRC need to amend the statutory code so that it's in line with their clarified position.
Statutory code does not have the same status as other legal opinion. While not being the law in itself, it carries a lot of legal weight. If you ended up in court in a discrimination case you would need to show a very good reason for not following the statutory code.
Here's what it says in Services, Public functions and Associations: Statutory Code of Practice:
------
13.57
If a service provider provides single- or separate sex services for women and men, or provides services differently to women and men, they should treat transsexual people according to the gender role in which they present. However, the Act does permit the service provider to provide a different service or exclude a person from the service who is proposing to undergo, is undergoing or who has undergone gender reassignment. This will only be lawful where the exclusion is a proportionate means of achieving a legitimate.
13.58
The intention is to ensure that the transsexual person is treated in a way that best meets their needs. Service providers need to be aware that transsexual people may need access to services relating to their birth sex which are otherwise provided only to people of that sex. For example, a transsexual man may need access to breast screening or gynaecological services. In order to protect the privacy of all users, it is recommended that the service provider should discuss with any transsexual service users the best way to enable them to have access to the service.
13.59
Service providers should be aware that where a transsexual person is visually and for all practical purposes indistinguishable from a non-transsexual person of that gender, they should normally be treated according to their acquired gender, unless there are strong reasons to the contrary.
13.60
As stated at the beginning of this chapter, any exception to the prohibition of discrimination must be applied as restrictively as possible and the denial of a service to a transsexual person should only occur in exceptional circumstances. A service provider can have a policy on provision of the service to transsexual users but should apply this policy on a case-by-case basis in order to determine whether the exclusion of a transsexual person is proportionate in the individual circumstances. Service providers will need to balance the need of the transsexual person for the service and the detriment to them if they are denied access, against the needs of other service users and any detriment that may affect them if the transsexual person has access to the service. To do this will often require discussion with service users (maintaining confidentiality for the transsexual service user). Care should be taken in each case to avoid a decision based on ignorance or prejudice. Also, the provider will need to show that a less discriminatory way to achieve the objective was not available.
-------
EHRC consulted when drawing up the codes of practice (see pics for relevant bits of the post consultation report). Press for Change and GIRES both participated in the consultation, as did an organisation called a:gender - 'a network that embraces transsexual, transgender and intersex staff from across the whole Civil Service.' 
I don't know if they're still active, their website doesn't give much away, but from their info sheet:
Members
This includes, but is not limited to, anyone who is or identifies as Trans, Transgender, Transsexual, Non-Binary, Gender Fluid, Genderqueer, Gender Variant, Cross-dresser, Genderless, Third gender or Bigender, and anyone who is Intersex. You do not have to be ‘out’ in the workplace to become a member. We maintain absolute discretion when contacting members
also ...
We liaise and attend internal meetings with Civil Service departments and external meetings on behalf of the Civil Service, such as with providers of support for Trans and Intersex people (e.g. GIRES, Stonewall, Mermaids).