Vanilla = official TPT version 93.3
Mods = mods such as jacob1's mod, Cyens toy, realistic physics mod, etc.
Scripts = Lua scripts added to powder toy. You can load scripts on vanilla TPT. TPT still is vanilla even with scripts. Some don't have much effect and won't change the simulation, so it's still vanilla.
Scripts can have custom elements though, those elements would be non-vanilla. They can exist alongside vanilla TPT elements.