Can the API have a reference to all the potion instances? I have a potion, that would give the player some warp ward as a side effect (among other things), but the only way to get that reference is by going into your internals.

Potion warpWard = Potion.REGISTRY.getObject(new ResourceLocation("thaumcraft:warpward"));

From a quick peek at Botania. You could also use Forge's object holders.

And you're correct.