You are definitely not meant to mess with the innards of the .bin
.
The paths are relative to the USB root (i.e., what you see over mass storage), hence the distinct lack of initial /
.
So that'd be a resounding yes to 2., and as for 1., they resolve to /mnt/us/usbnet/... from inside the Kindle's OS.
About 3., sky's the limit on a jailbroken device (once you know that the rootfs is mounted RO for safety, a fact made abundantly clear on your first connection to a login shell), but for what I think you're asking, essentially no
.