I was thinking about it, there are a few ways:
1) Enabled (whitelist) things. Logistic networks and biter/enemy resistances come to mind as the main, if not only, things people would care about.
2) Disabled (blacklist) things. Ignore trees and rocks, but that doesn't prevent the 'flickering' in someone's base.
3) User toggle. I can make it a keybind. Never made a shortcut but seems simple.
Opinions? 1 and 2 would be in the Mod->User settings. I don't want to make a GUI for this :P