Here are some things I've tried:
Concerning the NPCs, I found an item in the config called NPC rarity which, when set to 0, is supposed to prevent all NPC spawns (that's what it says when you hover over it anyway), but that didn't work at all. This may just be a bug though, and if any of you say that it might be I can create a ticket in the issue tracker for it.
As for Pixelmon spawns, I've tried editing the "Dimensions to spawn in" setting to have nothing there, but it seems when you delete all possible dimensions it just adds the overworld to the list. The other thing I've tried was disabling all 5 of the generations, but it turns out that doesn't actually disable the spawns. What it really does is allow them to spawn still, but then despawns any pokemon whose generation is set to false once it despawns. That sounds fine on paper, but really what it does is hundreds of pixelmon to spawn in quick succession for an instant and disappear, which looks really weird and causes a bit of lag.
So basically what I'm getting at is that I can't find an option, if there is one, to just prevent all natural pixelmon spawns, or one for all natural NPC spawns. If one doesn't exist, then maybe I'll make a suggestion for it, but i didn't want to jump straight into the suggestions forum without asking whether they existed already or not. I think both of those would function well as additions to /gamerule
Any help you all can offer would be appreciated. Thanks :D