CM handles this sort of this perfectly. Namely with weeds/xeno tiles.
1) Plant the Glowshroom / Shadowshroom down.
2) That placement will be the HQ, and slightly thicker than the rest around it - to help players identify.
3) Attack that HQ, and progressively have all the glowshroom/shadowshroom spawned from that 1, be killed.
IC way would be the HQ sacrifice the spawns it made, to protect itself. Eventually dying.
It can remain the same, but be easier to destroy as an antag / shadowling.
Less obnoxious to hunt down.
So you're not hitting shroom 55, and 56, 57, 58, 59 spawn.
Alternatively have it be like a supply chain. Where you have to feed the Shrooms nutrient/water - to further its growth and spread.
Like a supply chain.
That way you can cut it off at idk Botany, or 5 HQs down, and it'll kill HQ 6-30 if not reconnected.
Odd language use, odd temrinology etc. But I think they are fine as is, in terms of purpose.
They REALLY REALLY just need a way to delete, via players. Easier.