Hi, Stephen,
The Bootloader ROM is truly ROM burned at the factory and can't be modified in any way (burned once and done),but I think you can ignore the internal ROM bootloader, and burn your own bootloader into high address flash, have the DSC enter your own Flash bootloader after Reset as you have done.
Pls refer to the section 6.3.2 Start-up Process, it tells you how to bypass the internal ROM bootloader and jump to your own flash bootloader.
"
The FOPT register determines the boot source. The FOPT register is loaded from the
flash configuration field at address 0x40D in flash memory. The value of
FOPT[7:6]&(~SIM_BOOT_MODE_OVERRIDE[BOOT_OVERRIDE]) determines the
boot option: value 11b means booting from ROM, while any other value means booting
from flash.
"
Hope it can help you
BR
XiangJun Rong