In terms of planar topology, the Ethereal Plane butts right up against the Material. And given that it’s stocked chock full of phase spiders, xills, night hags, and undead, that means the Ethereal Plane is simply too close for comfort.
At CR 5, phase spiders are likely PCs’ first encounters with creatures able to ethereal jaunt, and if they don’t have the right magic on their side that can make phase spiders pretty scary opponents. Fortunately, phase spiders neutral creatures, so provided PCs can hurt one or parley with it, not every encounter has to be a battle. But a few encounters can go a long way toward introducing adventurers to the wild realities that lie just outside their range of perception…and convince them they need to prepare more spells than just damage-dealers—and pronto. Better to learn that lesson early, before the xills and hags show up…
Worldbuilding-wise, you need to do some work to establish a) what phase spiders want, and b) if what they want is food or conquest, what keeps them from just constantly jumping over to the Material Plane to get it? (In Golarion, the vigilance of blink dogs plus their own struggle with the xills both do the trick). That said, phase spiders work well in most campaigns—creepy human(ish)-headed spiders are great monsters pretty much across the board. They fit Middle-earth as well as they do Bas-Lag, and would do just as well for a planet-hopping campaign as a plane-hopping one.
Eagleheart is attempting a delegation to one of the mysterious glowing cities of the d’ziriaks, fostering trade between the Material and Shadow Planes. Deeds as well as gifts would smooth negotiations, and it just so happens the insectile d’ziriaks have a phase spider problem that needs clearing up: A large cluster of the ethereal-jaunting predators has been using the d’ziriak city of W’zorij as a pantry.
A blink dog sage warns of dire times ahead. One of his visions features a web in a land of mists that traps animate dreams like flies. Before he can elaborate, phase spiders attack his pack’s den.
The phase spider Chelicera is an obnoxious, caustic rogue with an obsession with gambling. Having been tossed out of the Goblin’s Gizzard Casino (losing a leg in the process, though it will grow back), he plans to settle the score with a heist. He needs accomplices for the caper; meanwhile, the casino is advertising for enforcers that specialize in bouncing otherworldly spooks.
—Pathfinder Bestiary 226
Pathfinder’s blink dog/phase spider rivalry is a much better one than the blink dog/displacer beast rivalry in older editions of the world’s oldest role-playing game. Blink dogs and phase spiders move through reality in similar ways, whereas the other pairing is just cats vs. dogs with some magic thrown in (and makes little sense, given blink dogs’ greater intelligence).
Also, uwtartarus weighs in on the phantom fungus. (PS: I love his name. I imagine it as the world’s most terrible college: “I go to the University of Washington at Tartarus. Yeah, it’s pretty hard to get off campus.”)