I think in this case it is just a generalisation of the (longstanding) way HCPs are trained to refer to "men who have sex with men." It's actually a very important way of framing advice leaflets from an epidemiological perspective, because the HIV virus doesn't care whether you are an out-and-proud gay man, or a closeted man doing the odd bit of cottaging while saying "I'm not gay because I have a girlfriend, this is just an itch I have to scratch from time to time." Both sets of men have to know to use condoms.
And arguably (following on from that tragic case in America where the transman got left with a complicated labour because they presented at A&E having only realised they were pregnant that morning, and got ignored until the baby was delivered still-born) there is a need for "if you have a vagina and your partner has a penis, regardless of what you call yourselves, you need condoms" advice, because some people are so deeply wedded to reality-denial they will do all sorts of absurd things, sometimes with really terrible consequences.