You're right that its odd to assume that people specifying pronouns are cisgender. I guess there are two reasons for that assumption.
Firstly, 100% of the people specifying pronouns very obviously identify as the prescribed gender. For example, Robert looks and sounds like a guy and specifies he/him. Ain't no one gonna misgender him. Ok it's an assumption to say that he's cisgender but one with an extraordinarily high probability of being correct.
The second reason is just my own attitude I guess. It's impossible for me to know what I would do if I were trans or had gender dysphoria, but I suspect that while I would be proud of being uniquely me, and happy to share that with close colleagues, I wouldn't broadcast it because it's just not relevant. I honestly genuinely believe that if I suffered gender dysphoria, I would just kinda swallow that rather than inserting it into the complex and delicate matters that I email people about. If someone at the revenue service misgenders me while deciding whether to waive $100k in penalties and interest for a client, I just wouldn't care because that person doesn't know me and what they think of me says more about them and their relationship to me than it says about me.
In this context, I assume people with gender dysphoria don't publish it, and that most people who do include pronouns in email footers have vanilla pronouns and include them to normalise the practice.
It's also not really a bug bear per se. I'm a grumpy jaded old man and I'm fairly critical of most things. Yesterday I got a bit ranty about names of things on google maps. Because I spend so much time reading and writing emails, I'm naturally critical of all authors, and footers in particular. Maybe I'm weird but I could talk about disclaimers included in email footers for hours.