I was able to craft Gaia Spirit seeds after killing the Gaia spirit from Botania, but can't grow the seeds as they require a Gaia spirit crux to grow. There is no crafting recipe for the crux though.

You will also need to remove the event.hide in client_scripts>jei_hide.js for it to show in jei again

Also of note there was a PR made yesterday to remove the seed and crux, so the ATM team may intend to remove it, and future versions of the pack may use different methods to remove the seed/crux

The crux was removed in kubejs and has not been enabled again. I am not sure if anyone has tested adding it again, but you can try removing the line of code in kubejs>server_scripts>mods>mysticalagriculture>crafting.js to enable the recipe

Appreciate the information. Thanks!