When i was Reading the lore it stated that the fungal was mostly underground (correct me if i am wrong) so it would make sense to have stuff like fungal labs, basements, and subways.
They would be places where the fungal roots(?) broke through and is now spreading fungus through the underground structure. Destroying roots could cause the fungal species to recede(trying to think of a different way do "defeat the fungus’ that one is not the best)And when the “benefits” Kevin mentioned(not sure when) for allying with the fungus could be obtained…
just a idea i had for when the fungus get a expansion, I apologize if this has been discussed before.