Hello.
Most actions, which add data into Lexicon (Lexica Botania), work in two game phases: initialization and late initialization.
But: Botania creates all lexicon stuff in init phase. And Botania loads after ModTweaker.
Summary: ModTweaker attempts to interact with Lexicon before one is created.

Simple example:
This line of code attempts to find lexicon entry. And it runs in init phase (as Craft-/ModTweaker log says). As result - it fails, because Lexicon isn't loaded yet.

I suggest to move all such code into corresponding Action classes, like it's done for removal actions.

Tested with latest version of CraftTweaker (cloned from this repo).
P. S. @Shadows-of-Fire AFAIK, It's your PR. Did you tested this part?