I was reading through the bootloader schemes at http://leaflabs.com/docs/bootloader.html and wondered if leaflabs ever considered a pure usb-to-serial bootloader.
ST Micro gives an example of IAP (in application programming) which uses the RS232 port (AN2557 : see below for link). In their application note, they use the standard ymodem protocol.
Instead of using the RS232 port, you could use the same method via the usb-to-serial interface. DTR / Reset would cause the maple to go into upgrade mode for a few seconds. If it detects the ymodem protocol, it would start the upgrade process. If nothing happened, it would proceed to run the user application.
The advantage is that you wouldn't have to switch from DFU to virtual com port drivers.