In answer to your question, I think the issue is that because the firmware is encrypted, it's impossible to check how it initialises the hardware and how it actually "gets its boots on". The documentation for the PortalPlayer chipset used in the iPods is not publicly available, so the only way to get a handle on how it all works is to look at how the manufacturer's firmware does things.
As much as I love Rockbox, and I couldn't imagine using a player that doesn't have it, I also can't imagine why anyone would choose to use a firmware that would preclude Apple's beautiful touch UI (I am thinking of the iTouch here).