Mordaunt did a lot of Stonewall related stuff whilst a junior minister at the MoD. Her position over the trans stuff predates her appointment as women and equalities. I looked into it when she got the job and was concerned.
She might have been continuing the work already done - but Justine Greening before she was sacked was starting to make noises that there was a problem (she acknowledged the importance of EA if memory serves correctly).
Mordaunt when she stepped into the job, went back to a more Stonewall aligned position and a harder line than the one Greening looked about to follow.
This MIGHT have been set up cynical by the Tory party to trigger a backlash (the culture war stuff in the US had demonstrated that it had worked for Trump). But that would also require Mordaunt being set up to fail by May from the word go. I don't believe May is that much of a masterplanner (exhibit a: Brexit shambles exhibit b: the general election). Plus the trans stuff wouldn't have been on her radar as she's been so busy firefighting everything else.