the maintainer considered using gender neutral pronouns “personal politics”

In this case, yes. Context matters a lot here, and the context is that this didn't refer to any human user, but a system user.

What's the gender of root? The question doesn't make sense, because root isn't alive, it's a technical concept. What gender is your PC? A directory? It's the same idea, it doesn't make sense.

However, switching it from one pronoun to another is politically motivated in the sense that it's virtue signaling a certain brand of inclusiveness. The only gender that could make sense is whatever is used most frequently, e.g. w/ ships we use "she/her" for whatever reason, despite gender having absolutely no reason to exist. If a gender is used, I've seen the masculine, but again, that's incredibly rare because any technical writer worth their salt would avoid the use of genders altogether because it doesn't make sense to use a gender in that context.

And why would he need to clarify anything? The simplest explanation is that this person is knee-jerk reacting to pronouns, and trying to change something that doesn't matter at all because they see pronoun and think "must be gender neutral." If they took a couple seconds to think, they would've realized that gender doesn't matter at all here. It's a useless change, and the reviewer shouldn't spend any time on it at all.

I've rejected tons of minor changes (e.g. whitespace changes) because it seemed the user was just looking to get their name in the commit log to build a resume or something. That's a waste of everyone's time, and this change looks no different.

It’s why every style guide (APA, Chicago, IEEE, etc) recommends sticking to active voice, especially in the context of ‘doing things’.

Yeah, that makes sense for most things, but for technical writing, the most important thing is clarity. Throwing a gender where it doesn't belong is a distraction, and using active voice where it doesn't belong is as well.

Check out The Elements of Nonsexist Usage: A Guide to Inclusive Spoken and Written English, in Chapter 4 the author recommends exactly what I've outlined here: use "the user" instead of "he/she." Here's as Stack Exchange discussion about just that (which mentions this book):

Replace gender-specific possessive pronouns with "the." Instead of "When the user types his password..." try "When the user types the password."

If the PR removed gender entirely, it would've had a better change of being considered. It's still a largely worthless PR though, unless it's fixing something tangible in the documentation.