Currently, EMI has support for making world specific configurations vs. a global instance-wide configuration. My suggestion would be to take this same concept, only based off of a user-defined set exclusively for recipe defaults.

Within the EMI Config UI, there would be a "Default Sets" dropdown menu. Here, the user can select a "Create New" button, which gives the user the ability to create and name the Default Set. The user can then select the newly made set from the same dropdown menu, which would give the options of "Enable", "Rename", and "Delete", as well as two buttons to the left with up and down arrows. Enable would activate that set (in which the button corresponding to the set would be highlighted), Rename would allow the user to rename the set, Delete would delete the set (with a confirmation dialogue prompt), and the up/down arrows would change the order position of the set within the Default Sets dropdown menu. "Enable" would be replaced with "Disable" if you clicked on an already active Default Set, which would toggle that set off. Only one Set can be active at one time.

With the config aspect covered, onto the mechanics. Outside of Default Sets, the user can still enable/disable recipe defaults like usual. These defaults would be part of the world/global Universal Defaults, which will appear across all user made default sets. Inside Default Sets, any changes to a recipe default will be saved to that Default Set instead. These defaults take priority over the Universal Defaults if they conflict. When looking at recipes, the Recipe Default button will be a different color if that default came from the Universal Defaults, or from the currently active Default Set. Universal Default recipes will have two color shades, one when it is in use, and another when the currently active Default Set has a different recipe defaulted and is overriding the Universal Default recipe.

Each Default Set will be stored as a separate .json file, containing the list of recipe defaults within the set as well as the name of the set.

In the main EMI config file, there will be a new variable for "Active Default Set", which points to the currently active set (or None if none are active and only the Universal Defaults are in use).

The benefits to this suggestion are twofold: First, it gives users the ability to configure multiple sets of default recipes for different purposes or different points of game progression. Second, it gives modpack authors the ability to predefine recipe defaults as well, including for different packmodes, progression points, or other organizational methods. This would be especially helpful for large tech mods/modpacks which have more efficient recipes farther you are in their progression (Mekanism, GregTech, Ex Nihilo, etc.).

Thank you for reading, and I hope you take this into consideration.

-Piano