Migrating devices - Power and Ground on I/Os?

You can bypass the fitter error by using the "Output Toggle Rate" assignment, give it a value of "0 MHz" for any of your user assigned VCC or GND I/O pins. This tells the fitter that the output never toggles, thus it won't violate the Vref rule.

Whether you assign the pin as a programmable ground, or let Quartus II do it by assigning all unused pins as outputs driving ground, you will have the same result as far as reducing SSN. The nice thing about user programmed pins is you can assign some to VCC to help with VCC sag. But you're right, ground bounce is typically worse than VCC sag.