One last thought... does the PIC bootloader even support updating the fpga flash chip? Thought it was only for updating firmware.
You're right, the bootloader is quite small (fits in the first few pages of flash) and it only does the firmware upgrades. If the bootloader did the flash updates too, we couldn't add support for new ROM chips without a bootloader update.
The command to jump to bootloader helps people who don't have the ICSP header, it also makes an all-in-one upgrade app possible.
I really like this app, I use it for a lot of FPGA development :) Firmware stuff though, is usually done directly with a debugger.