That's an odd way of defining "unusable." I have a couple of Pis with 3.5" displays that mount on the GPIO header and I have no trouble using those Pis in the way I intend.
I should point out that the 3.5" screen that I use have "pass through" on the GPIO pins that the display doesn't use. One of them even has header pins installed (mind you, I consider that to be a bad design for my uses, and for that--and other reasons--it is not my preferred display).
Still...there is a solution to your "problem". In the 5" screen space, you can get displays that work from the HDMI connector, leaving the GPIO header free for any other use you may have for it.