Currently its not possible to run prodigytech without patchouli being installed aswell. Would it be possible to make it a optional dependency?
It would be good for packmakers when they decide to alter a lot of the mods progression by changing or removing recipes. Because if they do that a lot of the information in the guide would be misleading and would confuse the player.

just get rid of the crafting recipe of the guidebooks?

using a mod such as Resource Loader (or shipping your modpack with a resource pack enabled by default) you can modify the contents of a patchouli book to correct the information that is no longer relevant.

perhaps a bit more effort than most people would expend on a modpack, but a solution nonetheless.