Difference Between Reserving Unused Pins via Device Settings and Pin Planner

Yeah, unused pins are reserved as "input tri-stated with weak pull-up."

When I assign signals to pins in Pin Planner and leave the signals out of the hdl, missing signal warnings are generated by the fitter, but the pins are in fact tri-stated. This is my first time using Altera and figured the preferred way of reserving pins is to mark them as reserved in Pin Planner rather than leaving their signals out of the hdl and letting them default to whatever the unused pins design setting is. However, reserving pins as "input tri-stated" in Pin Planner generates a different programming file and is electrically different than assigning a signal to a pin in Pin Planner, leaving the signal out of the hdl, and setting unused pins to "input tri-stated with weak pull-up" in design settings. This is what is confusing me.