it’s highly personal, so ideally you ask the individual and include their consent in your article. that said, generally speaking, trans people will use their current pronouns, even referring to their pre-transition selves. this is also what’s generally considered polite if you don’t know them, so it’s pretty suspect that the article is not doing that
still, something about malice and incompetence…
rather than talk about my experience, i tend to think it’s more helpful to have cisgender people imagine themselves in similar hypothetical situations:
imagine everyone in your life started using she/her pronouns for you. how would this make you feel? how does this affect how you react to them? how does this affect how they react to you?
imagine you woke up in a female body. how would you feel? imagine you had to adjust to it for a week. then a month. then a year. then ten years. what adjustments to your life would you have to make? how does this affect how people treat you? how does this affect your behavior? how would you feel about this situation? what would you miss about your previous body?
the second experience is essentially what it’s like to be a transgender man, except it’s from birth and you don’t (necessarily) get to start with the knowledge you’re a guy (some people more intuitively figure it out than others)
these questions hopefully help you develop a sense of what gender means to you, which should help you understand what gender means to us (obv it’s not the same for everyone, and it’s pretty binary, but it’s a decent starting point)
i would have appreciated hearing how the author, personally, found capitalized pronouns to be affirming, because, absent that reasoning, it really does seem like it’s to set up a deferential power dynamic. i don’t really mind respecting the pronouns anyways, but it does mean i don’t really want to be friends with Them until i understand what’s going on there better