As far as I know: (Haven't gotten my hands dirty in the L4D2 Authoring Tools yet)
Custom model skins: Textures yes, if you overwrite the files in the materials folder for your addon. Custom infected models, yes, if you make a new entry for infected populations that includes them.
Update: According to the VDC, custom infected populations are not supported properly with addons, so do that at your own risk.
Survivors start with no weapons: I don't think so, though you could try using a weaponstrip. As far as I know, having the pistol is mandatory unless you replace it with a melee weapon ingame.
Flashlight: No.
Health/Behavior: No.
Level w/o special infected: I beleive there is either a volume or navmesh option that can prohibit special infected from spawning. But you'd have to cover the entire map with it. Or use
this.
Again, I don't really know what I'm doing, the above is just speculation combined with what I remember from the documentation on the VDC, so that might all be wrong, and there is some scripting involved in my answers (The infected populations) which some might count as modding. I left it in because there's not really any code involved.