Thunder is just a separate flag that is on or off randomly. It will only be thunderstorm if it is also raining but the thunder flag won't turn rain on or off. The thunder flag will also stay on if you turn the rain off manually. You can see this by turning rain on right after and it will still be thunder. If a mod changes thunder directly this doesn't apply anymore, it forces the flag on or off.It does interest me whether thunderstorm can "replace" existing rain conditions, however. This in particular, is what I am unsure about as I have no idea how the thunderstorm code is written in minecraft.