Ok so this is a threepiece suggestion, but they're all interconnected so hear me out. If you want a quick TLDR, it's basically implementing AE2 autocrafting concepts for patterns / sending a recipe bill, but for NEI bookmarks.

First, within any NEI recipe screen, add a button that allows the user to set that specific recipe as the "default recipe" to make that output item. This takes into consideration both the currently set OreDict item, the specific catalyst being used if there are multiple catalyst types for that recipe (i.e. different machine tiers, different types of furnaces, etc.), and the tool that is used in that recipe (for cases like GT tools).

EMI has a similar concept (shown in the image below, the green heart dictates that recipe being the "Default Recipe").

Now with that in mind, onto my second suggestion: Default Recipe Presets.
Like with the new item grouping feature done for NEI, this would be the ability to make a preset for "defaulted" recipes, as well as the ability to name these presets & swap between the presets in game at any time. Having modpack support to pre-set the presets also would be nice here.
In a GTNH context, this could mean things like voltage tier specific default recipe presets (stone preset for iron plates is the hammer + 2 ingot crafting recipe, steam preset for iron plates is the steam forge hammer 3 ingots -> 2 plates recipe, LV preset for iron plates is the lv bender 1 ingot -> 1 plate recipe, etc.).

Lastly, the final suggestion is to have the ability to automatically "generate" a recipe group for any item directly within the NEI recipe screen, based on the currently set default recipes. Probably through a button in the recipe screen itself like before.

So for example, take the recipe below for EIO Reservoirs:

In it there are 3 different items: fused quarts, HV electric pumps, and a cauldron. For each, I could have the currently enabled default recipe preset determine that these three recipes are the active "defaults":

Therefore, upon pressing the button on the EIO Reservoir page, this here would automatically generate at once in one group (or possibly in one page depending on an NEI setting, which could be a good idea):

Hope this is a clear way to explain the suggestion here.

@slprime would there be any consideration in incorporating this into NEI?