Greetings,

have read around, and haven't found a way to do this easily without a ton of scripts.

it is possible to have a configuration option, to Hide all items/recipes until staged?

basically, nothing shows up (In JEI) until you add it to a stage (and the stage is unlocked).

Add additional option this this, would be "automatically set player to stage". This would allow a player to be added to a stage on first world join.

I think "automatically set player to stage" equal not using stage in first place.

Also you can hide all items from certain MOD

// Locks all items from a mod to a stage
mods.ItemStages.stageModItems("one", "minecraft");

I don't really see how this feature would be helpful. I have worked with a lot of pack devs, and it seems that they all use this as a way of tracking what is left to stage. With that said, you could write some very simple script to stage all the items to a default stage, and then stage them again afterwards to change them.

For example, you can use for mod in loadedMods to loop through the loaded mods, and then mods.ItemStages.stageModItems("default", modname); to stage everything in that mod. Normally I don't mind adding features that I don't understand the usefulness of, however in this case it is very simple to do what you want with the existing tools.