No. The ATmega's VCC determines what the voltage of an output pin will be. In all cases you mention, the input is either already 5v or regulated down to 5v before being connected to the ATMega's VCC.
So 9V on Vin will still result in the I/O pins being (about) 5V, because there is an on-board regulator that regulates the 9V down to 5V.