Two points to add here:
1 There is no legal requirement to acknowledge a claimed status of "non-binary", since NB has zero legal meaning in UK law.
2 UK Case Law has established that, where a person who claims protection via gender reassignment does not have a GRC [ie: has not legally changed their Birth Certificate] the legal comparator for a male at any stage in any process of transition is other males; the legal comparator for a female is other females.
See [from 2003; pre-GRA 2004] www.casemine.com/judgement/uk/5b46f1fa2c94e0775e7ef4e3 [paras 70 onward]
and this case above was relied upon in 2013 [post GRA 2004] in this subsequent case:
www.casemine.com/judgement/uk/5a8ff7bb60d03e7f57eb1a1f [see paras 63 - 68]
So, there is no need to alter any facilities and given the requirements of The Workplace (Health, Safety and Welfare) Regulations 1992 it is very unwise of this employer to have made such an adjustment.
Even if a person has a GRC this does not give that person any legal right to access any facilities for the sex transitioned to. It is probably a better legal option for any employer to allocate a third, separate facility to such a person.
Schedule 3, sections 26, 27 and 28 are explicit about this:
www.legislation.gov.uk/ukpga/2010/15/schedule/3