What I mean by that is according to the code in the class here: https://github.com/Snownee/Cuisine/blob/master/src/main/java/snownee/cuisine/events/BetterHarvest.java
That it sets the blockstate according to the item dropped, if it's a valid plantable, which may or may not be the actual crop item returned from the harvest.
Example: You have a modded crop that returns a random vanilla food item when harvested. This mod will assume that the carrot/wheat/potato are actually the crop themselves, and set the blockstate accordingly, thus replacing the modded crop with carrot/seeds/potato crop, respectively.

The other thing to note here is that the rightclick harvesting system just flat out assumes that every single instances of BlockCrops are allowed to be click-harvested in this way, which can not be true in many cases, and that there are no config option to turn this behavior off, or at least a blacklist system.

Minecraft version: 1.12.2
Mod version: 0.3.9-build678