As the EHRC guidance stated that it applies in Scotland, this looks like something of a backtrack from the Scottish government:
"A spokesman for the Scottish government said: “Our support for trans rights does not conflict with our continued strong commitment to uphold the rights and protections that women and girls currently have under the 2010 Equality Act, which includes a number of exceptions which allow for trans people to be excluded when this is a proportionate means of achieving a legitimate aim. Those exceptions are important and the Scottish government supports them.”"
It does contrast with this:
"However, in an official statement on its website the Scottish government acknowledges that trans women have gained access to single-sex services despite Equality Act exceptions."
But it looks like they are not going to argue with the EHRC (that's how I read it).
As for the no comment/decline to comment/didn't have a comment from the three groups - shame on them. They have one job and they're meant to do it for women and girls.