Link to a FAQ
(G)ufw allows traffic to come in through that port. But it doesn't check who receives it. Choosing Transmission on the GUI is just the easy way for the users to open transmission's port. You can achieve the same by opening transmission, looking for the port on the config, and opening it with Gufw.
But, as 2 applications can't listen on the same port simultaneously, if you are running transmission all of the time, you can be pretty sure transmission gets the traffic :)
Hope this clarification helps!
Thanks Emilio, that solved my question.