I could write a MineTweaker script to achieve this but I'd rather have an option in the config for ease of use and less chance that the script would cause unforeseen issues.

A friend suggested this to me too, 1 problem is that the machine is used in the deflector recipe. I think a good solution is to make a generic item that I can make all my crafting recipes use, that way I have safety from recipe conflicts and can also add the ability to disable weather machine.

That sounds like a great idea! And TBH I was going to disable the weather deflector as well if at all possible, as I've disabled block damage, but I still like seeing people get tossed around like a sack of potatoes. 😄

Edit: Side note, would it be possible for me to edit the configs in a way to lower the frequency of Tornadoes/Cyclones while increasing the chances that they spawn in at increased strength, ie. a F3? I haven't looked at the configs yet for a way to do this, I just wanted to ask first if it was at all possible.

Less storms: Player_Storm_Deadly_OddsTo1, Player_Storm_Deadly_TimeBetweenInTicks

Make progression more likely once storm formed: Storm_OddsTo1OfProgressionBase, Storm_OddsTo1OfProgressionStageMultiplier

At some point in either 1.10 or 1.12 I added a config option for every recipe in Misc.cfg, eg Block_WeatherDeflectorNoRecipe, I also redid all the recipes to use a base weather item. so all good now.