I have a single, objective reason: narrative integrity. To expand upon this, the more varied the people who are utterly suffering, the more it underlines and amplifies that suffering and the context which generates it. That should be enough even just from a literary perspective.

Also, edit to add: the dystopia in 40k isn't concerned with who you are, just that you accept full servitude to the Imperium. I honestly couldn't see most Black Ship attendants hating a trans psyker any more than a cis one. Nor would the Astra Militarum ever turn its nose on fodder just because one uses different pronouns.

And that's exactly the point! Let it be a fully inclusionary dystopia! Let the Imperium's complete and utter disregard for a person's individuality oppress everyone. This dystopia is literally religious cyberpunk, where they've replaced The Corporation with The Religion. And Big E didn't care who or what you were as long as you obeyed orders, that is clear throughout all existing doctrines across the Imperium's infrastructure. Everyone is meat.

Approaching it from the opposite direction, 40k is supposed to be a dystopia, why would you want gender equality and all that nice stuff in a dystopia, unless you thought it was dystopian?

Representation is not about being moral, it's about being audience-inclusive. If there's no reason not to be inclusive of a sector of your audience, then refusing to do so simply makes large portions of the audience feel less welcome enjoying the work.

Or if you are stuck between orks on the south and tyranids on the north, do you really care about bathrooms at that point?