I agree, people who are unable/unwilling to get both toys will prefer the MP over the 3rd party upgrade. I know I do, the MP is the much better toy by far.
However that would only affect those who are only willing to get one toy of the character. It won't make a difference to those who want both for their MP and Classics shelves.
The FansProject release predates the announcement of MP Rodimus by a year or more so it's nothing to do with trying to cut into Hasbro's profits. However it is safe to say that the MP release will indeed cut into the Protector sales as not everyone is going to get both toys.