Possible to use the hardware serial port for peripheral on ATmega32u4 when using USB for programming?
I have a Teensy 2.0 with a ATmega32u4 and I can use both, with the USB as Serial.* and the hardware UART as Serial1.* 

For the Arduino Pro Micro it is the same.  See Arduino Pro Micro, get data out of Tx pin?

For Teensy, see https://www.pjrc.com/teensy/td_uart.html