This issue is a extention of "AE2 crafting plan" from the issues #657, #783 and #973.

Topic:
In the AE2 autocrafting feature Crafting Plan the EMI gui vanishes and can't be used to add items to favorites / to pin them.
See e.g. #657 for screenshots. The first issue stated, it is an AE2 problem with mod integration.

On the other side: In AppliedEnergistics/Applied-Energistics-2#8401 it is stated to be the choise of EMI to render or not.

To give more context, i have tested 3 szenarios:

• using only JEI in 1.20.1 (Forge) gui renders / items in the Crafting Plan can be bookmarked.
• using only JEI in 1.21.1 (Neoforge) no gui render / items in the Crafting Plan cannot be bookmarked. (AE2 changed something)
• adding the mod AE2 JEI Integration in 1.21.1 (Neoforge) gui renders / items can be bookmarked again.

Adding EMI to each of these szenarios, doesn't render the EMI gui on this screen.

The last szenario suggests the possibilty for mods to add them to this screen. (At least for 1.21.1)
So maybe EMI or an EMI addon mod could add / fix this feature.

Personally I am interested in a solution for Forge 1.20.1
There is a mod AE2 Crafting Tree, which adds a button to this screen. (The button opens an other gui, sadly EMI also doesn't render there.)
So there are other mods integrating in this screen.