I have been reading bootstrap's code and if I understand correctly, it is designed to boot a single game based on a certain configuration contained on plain text files, such as the game rom file path, settings and other given parameters. I see that it is being designed with portability in mind, so it will not depend exclusively of TM++ frontend, but also another frontends can be made for it, and these are the ones that should write these files to modify bootstrap's configuration parameters before being ran, so it can be used as a multi-rom loader, and given this logic, you can even configure any frontend to boot automatically into an specific rom upon launch, and I think TM++ has that feature already included.
For example, let's say someone adapts nds-boostrap to a PS3 menu themed like frontend. the frontend itself should be the one that can read-write and interpret the text settings files and make them user friendly, among other things such as the ability to read the rom file header so it can be shown as it currently is in TM++, then based on that configuration set, bootstrap would do the magic.
In less words, think of TM++ as the manager who says what to do, and nds bootstrap as the worker who knows what to do based on those orders.
This makes me think why no one else has made any other frontend or has ported another flashcard menus to this