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Rockbox is intended to be a fully functioning replacement software, so there was never an intent for it to be set up as secondary.
It was at the very start of the H1xx port but then was changed as developers got tired of having to hold REC to boot into Rockbox every time.
Of course, once you start the Apple firmware, it will continue to load until you reset the ipod.
The standard bootloader isn't going to get changed.You can either see if someone in the unsupported builds forum has a modified one, or you can try out Loader 2 (unsupported here though too).
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