To preface, I use the Player Request Crafting Layout. It creates a logistic request for every entity. I use it to make it so all relevant items could potentially be automatically requested or trashed and to have everything organized. Unfortunately, the logistic request gui has a limit on entity count. Since JQ adds 5 levels of each entity, it surpasses the limit in the gui.
To pare down on the amount of entities, I used the "disable quality" setting to disable everything that I didn't think I'd ever want to create at higher quality. I loaded up the game and learned that everything that I had disabled the quality for is no longer able to be hand crafted. Is this a bug or an engine issue? I tried to use a mod that allows hand crafting of everything, but that didn't work either.