Richard Morgan’s version of the Red Room was probably the most explicitly “it’s all a metaphor for the way men control women! with literal pheromones!” and even his version had a prominent female collaborator in Lyudmila. Who is the one who justifies (and possibly originated) the idea that Black Widows need to be sterile so that they can be warriors instead of mothers. Because the two things are opposites, you see.
Setting aside the fact that this might be something Richard Morgan Actually Believes, women are perfectly capable of being complicit in the oppression of women. That’s part of Natasha’s story too— the degree to which she can make up for a life of violence and espionage by doing more violence and espionage?
Samnee/Waid’s Headmistress is implicitly part of a larger Soviet/KGB operation. She’s getting her orders from men, and we know this because the USSR was run by men. Even when all the major players we see on panel are female, we understand that the Red Room isn’t Themyscira, that it is part of Man’s World, operating within a socio-political context where sexism exists.
Recluse’s operation is an exception to the rule in that she is, from what we see, operating independently, but Recluse is still very much the product of a cruel system, the comic book embodiment of the cycle of abuse. She’s obviously not over any of it.
So, I think the symbolic framework is flexible enough that women can be in positions of power in the Red Room even as the Red Room remains sort of an allegory for the ways the patriarchy turns women against themselves. It might muddy the metaphor a bit, but I think that’s probably a good thing, because it lets these stories be more than allegories, and leaves creators space to explore slightly different themes.