Here's everything I've noticed so far with the 3.1.0 alpha 2 build:
-Chrysopoeia name in JEI is currently tagged as "container.roots.transustantiation.name"
-Spell Recipes has a bad link to Herbs
-Saturate's warning text falls off the bottom of the book
-Scatter's ending punctuation is missing
-The bottom of Spring Storm's text is running into the book edge
-Shift-right-clicking a Pyre in creative mode overwrites what's in the Pyre
-Grove Supplication Ritual's name is currently tagged as "item.ritual_grove_supplication.name"
-Offering Plate text falls off the bottom of the block
-Offering Plate has a bad link to rituals
-Fey Fire's grammar structure unclear. Suggestion: change "...hostile creatures, animals and items unaffected." to "...hostile creatures, with animals and items left unaffected."
-Sylvan Armor text runs into the book edge
-Natural Resources has a bad link to rituals
Slightly bigger issues:
-Right-clicking any variant of Elemental Soil with any variant of Elemental Soil gives the player a dirt block(?) and doesn't consume the existing block, and can be repeated with the same type of elemental block to gain infinite dirt

Final point has been addressed.

Turns out Patchouli doesn't have the ability to link to categories directly, you must link to an entry. That's... so dumb.

Thanks!

The latter is something I'm aware of, I might file a separate issue for it.

-Shift-right-clicking a Pyre in creative mode overwrites what's in the Pyre

This is actually intentional, do you think it's problematic?

EDIT: So, I've addressed everything else and I'll do alpha3 some time tonight; curious about this question though.

In creative, not so much since anything accidentally lost that way can be rebuilt (say, accidentally adding off hand items to the Pyre). That might be something to raise as a separate issue- I don't think Botania or Thaumcraft put what's in the off hand directly onto their pedestals and altars. I need to double check what they do as I can't recall at the moment.