Fixed this in version 1.1.39.
I've looked into this, and it seems that marking a proto tree as faction-unique was slightly more rigid than it needed to be. Specifically, the recipe was required to be faction-unique, while marking the entity or item as faction-unique would break (if the respective recipe was not also marked). I've added code that, if the entity is faction-unique and the the item and recipe is not, the faction-uniqueness is copied to the others.