Well, there is a "Shaped Forestry" NEI recipe tab, so...

1. Create a new NEI recipe tab for EE3: call it "Transmutation" for example; that would show you all the recipes of how you can get chosen item using only Minium/Philosopher's stone (briefly: get rid of a whole lot of reduntant shapeless recipes, and place them on another NEI recipe tab)
2. NEI plugin for showing Calcinator recipes (when there would be any)
3. Add recipes for all other EE3's machines.

Not an issue