I just received 100 breakout boards with an ATmega32U4 for a course at Uppsala university from pcbgogo. The boards are on panels and I show you how I can quickly upload the bootloader using a rig which I made earlier.
I use a modified version of the Caterina bootloader the modifications are limited to the use of the indicator LEDs because my board only has one LED connected to pin PE6.

https://github.com/uwezi/Eduino

Links:

https://www.pcbgogo.com/
https://www.microchip.com/wwwproducts...
https://blog.zakkemble.net/avrdudess...
https://github.com/adafruit/Caterina...
https://www.fischl.de/usbasp/