Lovestruck Derpy is not related to Whooves and Assistant in any way other than the writer being the same person. They are not of the same universes.
I would like to think that people can trust my writing ability enough that I would know how to write other good companions other than Derpy. Or my voice acting ability, which is quite broad and certainly not limited to our googly eyed friend.
I am however glad that you like her, it means I did well, but still in Doctor Who it is always best to assume perhaps a possibility of other companions.
This does not confirm nor deny it happening in Whooves and Assistant, but just be weary of this fact.