Fungaloids can’t make new boss class fungi (towers, spires and giant flowers) yet, although that will likely get implemented eventually.
That said, a fungal bloom and two fungal flower locations in a close vicinity is a big deal, the flowers alone spread the fungus much faster than it normally would. To rub it in, giant fungal flowers are the hardest of the fungal queen trio to get rid of due to their massive fungal gas attack preventing you from just burning all of the grunts and then shooting down the boss.
Your options are either to hit the road in hope of finding a better place (literally any other place is better for a non Mycus pc then a fungal infestation) or stay and exterminate all fungaloids starting with the queens. If you choose fight over flight you should be prepared for an all out war that will take weeks to finish.