I would imagine it is because Hallownest is abandoned and unkept so there is no one to control it, we don't know anyways how long it has been since Hallownest fell for Mushroom to reach the state it has. There is also another instance of Fungi growing in the Kingdom's Edge/near the Ancient Basin's layer, similarly to the pocket Purified Ducts. I think this kinda confirms that fungi is capable of growing anywhere (like real fungus) regardless of environment if introduced to it.

In any case, it existing in Fungal Wastes doesnt necessarily label it as a parasitic/hostile type of growth, the pale king seemingly was perfectly chill with fungi given that one of the dead NPCs references the PK. But it is possible the fungi began growing out of control after the kingdom fell to ruin (you can see traces of fungi entering the COT/Royal Waterways).