This never happens if you only use the unix clipboard. I agree that both methods should point to the same clipboard, but this is an implementation detail. The important thing is the interface: selecting text copies it to the clipboard, middle-clicking pastes it.
Imagine you install a 'clapper' in your bedroom to control the lights. You say "works great for me, let's install this everywhere". Someone responsible for an auditorium then says "so clapping turns the lights on and off?"
That said, I frequently use text selection as a highlighter. I will highlight lines as I'm reading text to help me keep track of which line I'm on. I also need to select text to apply formatting such as bold or add link.
Super useful to have two different scratch buffers when moving things around.