No, there is absolutely no difference.
The FP3 has a (protective) cover like the FP2.
The bumper is just an add-on, that - interestingly - is not featured on any marketing picture I have seen so far. Just take a look at the Fairphone shop. It is a cover for the cover as well.
As is a screen protector for gorilla glas.
And, as you can see by the following thread, the cover can break. Protecting it therefore is not neccessarily a waste.