Thank you for the suggestion. I took a quick look but ended up using a work around instead:
Burned the bootloader via the ICSP using a USBasp programmer
Uploaded the sketch via the USB serial port
Dumped the flash to a flash.hex file using avrdude, via the USB serial port
(dumping the flash to a hex file using the USBasp did not work but for some reason dumping to a raw bin file seemed to)
Used the avrdude and the flash.hex file to program other boards via the ICSP using a USBasp programmer
This solved my problem but does not answer my initial question.
If others have been able to successfully use an exported binary with_bootloader, I would be interested to hear about it. My impression is that it is not an actively used feature that has a bug in its implementation.