Isn’t that already the default upload method for all ATMega32u4 based Arduinos, like the Pro Micro and Leonardo?
Anyways yes it’s supported since PIO invokes AVRDude which supports that what the Flip program (see your appnote) would do. Per artikel:atmega_u-howto:flashen_flip [Dokuwiki] it can be invoked with -c flip1 -P usb like
avrdude -c flip1 -p m32u2 -U flash:w:path_to_firmware.hex -P usb -v"
So as you can see in Atmel AVR — PlatformIO latest documentation I would try adding
upload_protocol = flip1
upload_flags =
-Pusb
to the platformio.ini.