Hello, @Dominic88
Thanks for you post.
I suggest using the same RTD during the development.
Regarding to the bootloader and the corresponding M7 application running on same M7_0, since bootloader fully quits and totally switched to the M7_0 application, it may not impact if different RTD used for bootloader and M7_0 application, but again, I suggest using the same RTD during the development work.
It is possible to change the RTD used for the bootloader, you may rebuild the bootloader using different RTD, but unlike the version that used in the AN, the other version are not verified and tested, there may be issues that need to be debugged during the integration.
For bootloader itself, the version that mentioned in the AN is relatively old, there are newer version for your reference which are based with newer version RTD.
BR
Chenyin