Configuring the unused pin in CPU
I think your cases 1a and 2a are the same thing.
If the pin is configured as an input, then shorting it to either Vcc or GND is pretty harmless.  If it's left floating, then you will get an indeterminate result in reading the pin.  The pin will be vulnerable to ESD (electrostatic discharge), but that's unlikely to matter so long as the board isn't touched.
If the pin is configured as an output, leaving it floating is harmless.  Forcing it to either Vcc or GND could damage the microprocessor.
Of course, if your board is so poorly made that the pull-up or pull-down resistors are either missing or shorted out, then you probably have much bigger problems to worry about.