Pin Planner - by board wire?

In general, you use the Pin Planner because you want to layout out your pins in specific locations because you're going to spind a board. So you know the flash will be placed in a specific location compared to the device, the data and address will go in a specific order, and so you place your pins that way.

Your addressing the problem where the board is already laid out, you just want to make sure your RTL I/O match the correct connectsions on the board. As mentioned, Tcl is probably the best way to do that. Just creating some variables to hold the translation:

set switch_5 PIN_A3

Then if you want my_input[5] on it, do:

set_location_assignment $switch_5 -to {my_input[5]}

You could then just source the Tcl file, or add it as a pre-flow script.

(Another option is to have a top-level RTL shell that has the correct port names and pin assignments. You would just use that to instantiate your HDL underneath, and hook my_input[5] of your code to the top-level port switch_5.)

Of course, this isn't very useful for a specific person since they would usually only do it once or twice. It could be useful if a lot of people use it, which I believe is your goal, but distribution like that is often difficult. Good luck.