I think the mushrooms almost feel too... mundane? The average person probably interacts with a lot more mushrooms than crystals. Crystals also have a long history of being associated with magical properties, and modern science has figured out some neat things that can be done with crystalline structures. We're pretty primed for crystals doing cool stuff. Mushrooms have significantly less mysticism associated with them and related science is more biological than technological. That's not really solidly in favor of one or the other, but it does mean the audience will more readily accept crystal hijinks with no warm up than mushroom hijinks with no warmup. The closest comparison to the mycelial network is Yggdrasil, which is solidly in the high fantasy category rather than sci-fi.
All that is to say, I think the mycelial network needed more time to set up than the show gave it. Some kind of foreshadowing, like simply mentioning something about advances in organic technology. Farscape probably would have been able to sell it pretty quick, but Farscape also has organic technology as a core part of the premise with Moya. Not an inherently bad concept, just kind of comes out of nowhere in the context of Trek.
I didn't like that part at all. An infinite multiverse, which they state in DSC is the case, means that anything with a probability greater than zero is guaranteed. Mathematically, the multiverse should have already been wiped out at some point. It's also a throwaway line meant to increase dramatic tension for all of ten seconds before the scene ends, and an empty threat given that following through would end the show.