Stonewall is not an LGBT organisation, it's a LGB organisation. They do not cover T issues in England (not sure about Wales) because there are other organisations focussed on those issues (such as Press for Change). They are an LGBT organisation in Scotland because there wasn't an equivalent T organisation there.

Whether Stonewall should cover T issues is another question. Personally, I* am dubious about this. In my experience, Stonewall is very LG with a very small b tacked on the end. I think to genuinely represent trans issues would require a cultural change in Stonewall and commitment to understanding trans issues, rather than just tagging another letter onto the website headers.

*I'm a cisgendered bisexual woman who's working on being a trans ally.