That isn't how it works. The presence of neutral allies doesn't somehow counterbalance and cancel out the transphobia. If a platform allows transphobic users - as Hacker News does because transphobia isn't against the guidelines - and transphobia is common in threads where trans issues or people are a subject (and it is) then it's a hostile platform to trans people.

Asking trans people to ignore this is like asking Jews to be comfortable in a bar where only ten percent of the patrons are Nazis. Arguing that "well not everyone is a Nazi" doesn't help, an attitude of "we're neutral about Nazis, we serve drinks to anyone" still makes it a Nazi bar, just implicitly rather than explicitly.