>
>
> I would have thought secure a soundly working bootloader
> first, then the other app can make it's own settings.


The point is that knowing what the safe settings for all the pins are, is
outside the scope of a bootloader. This would be different in every
application.  While the bootloader is running, and before the application
starts up, it's up to the designer to assure that all the pins are in safe
states, and to know what those states are, dependent on the hardware
connected.
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