Simple logic might not resolve the issue, but social dynamics and "human" nature starts to reveal more about the situation.
1. The Shellbrood are nightmarish, abysmal, in-your-face, mean f$&kers. The average person would be ripped to shreds by them in an instant. Think of "Alien", then think of one on one confrontations... a human whose only weapons are the surviving technologies they have (with limited shots/ammo), and their wits - versus - a biomechanical monstrosity designed to hunt and kill, with natural armour that can shrug off most minor damage and provide limited resistance to blows that would kill a nautal being, with natural claws and teeth that can shred flesh, and organic acids that eat through armour. Now imagine hundreds of them in a concentrated location, often drawn to the power supplies of downed ships. It's a war of attrition where the Shellbrood are constantly restocked with new numbers and the survivors have dwindling reserves. Any long term advantage that the survivors might acquire is bound to be considered.
2. Looking at the numbers... With enough exposure, a survivor's regeneration factor is roughly modified up or down by a factor of 12-14, but regeneration is only a small part of a person's oveall abilities. Strength would go up for the females because they can train harder and do more things before fatigue sets in. Synaptic relays would beapable of firing at full speed for longer, and dexterity might be mildly increased also. Mental faculties aren't necessarily affected, except maybe for the ability to study longer before fatigue factors apply. Social abilities aren't affected.
Let's say a "Typical" Shellbrood warrior is rougly a match for two survivors working together (building traps, laying ambush, flanking tactics, etc.), and combining all factors let's say the regenerative factors increases females to triple their previous power level, and reduce males to a third of their previous level. According to base numbers, 10 "Typical" Shellbrood are a match for 20 survivors. If half the survivors are female, half male (female power = 10 x 3, male power = 10 / 3... Total power = 33.333), the benefit from the mushrooms is over 66% in comparative power levels. That's more resources that the survivors can use for surviving, rather than expending them on fighting the 'Brood. The thing is, that there are a lot more Shellbrood in the darkness, and they rapidly spawn to an equilibrium point in their predatory niche, if their numbers in an area are halved, it will only be a year or two before they are back up to full strength (and quite often a sizeable portion of the Shellbrood will remain hidden for this very reason). Only if they are completely eradicated will an area be safe for an extended period...and even then, there will be other nests of Shellbrood looking to expand into the vacated territory. More Shellbrood die to violence from their own kind than from survivors in the hive.
3. Once biomatter has been impregnated by the Manbane spores, it is effectively a permanent change in the flesh. Adult males who might want to improve things by stripping the fungus from a region will see no benefit from their efforts, even if their sons might. Look at the powerful men in our world who seestatistical data regarding climate change and refuse to do anything about it because it might make their lives a bit less comfortable now. Combine this with the fact that females in this setting are more powerful, specific females wouldn't want to lose their competitive edge to return to a patriarchy, and generally society is now stacked against males... the Manbane isn't disappearing in a hurry, especially when Shellbrood are a constant menace, and wars break out between neighbouring towns and secretive factions in the darkest passageways.
4. There are probably settlements filled with the dead in hidden parts of the Darkhive. These would be places where the Manbane had been purged. Women had lost their "superhuman" abilities, thus allowing the men to take charge through revolution, and the Sheelbrood (or aggressive matriarchal neighbours) had simply wiped them out. Such locations become apocryphal tales and warnings to explain why the Manbane must be allowed to grow, and why men must remain "in their place". This is a deliberately subversive setting.
If I'm turning you off with all this gender politics, I'm sorry but this obviously just isn't the setting for you.
In the vein of "Disney Princesses turned on their heads", I'm definitely seeing stories like a gender flipped "Mulan". Where a young boy masquerades as a woman to join the army, using cunning and strategy where brawn is unable to win the day... Maybe he might even marry the General when his identity is revealed, more likely it is revealed that he has XXY chromosomes and is a genetic abberation who gains neither the female's regeneration nor the male's weakness and may be infertile due to a cruel twist in the narrative designed to prevent young boys from getting their hopes up).
This setting is tense, it is dangerous, but while a similar "Male-centric" setting could be overly testosterone filled (see Warhammer 40k), this setting is more about cycles... Birth, death, renewal, pushing against the cycles to make a difference and accepting the ramifications that come from the difference. Tears of happiness, tears of frustrations, tears for fears, tears of despair.