Arduino IDE Board Selection for 32u4 on custom PCB
There should not be any difference, However you would need to load the ItsyBitsy bootloader instead of the ProMicro Bootloader. Personally, I use the Pro Micro Bootloader on my 32u4 Boards.

The only difference would be in the size of each bootloader, one may be smaller and give you more actual codespace. Other than that there should be no performance difference because your code runs independently of the bootloader.