It's become standard etiquette/respect/decency to use the pronouns preferred by the subject. Yes, it's an adjustment for us "old" folks over ~30 or so, but it gets easier with exposure and mindfulness.
The author of the article in question isn't writing about trans persons in particular; you're trying to create a problem where there is none.
> Did the author imply trans students don't exist
No. Neither did the author imply that boys don't exist by using the pronoun "she". Only an intentionally uncharitable reading would lead one to that conclusion. Again, you're trying to create a problem where there is none.