1. kernel and the rootfs are two of the partitions in the NAND chip. rootfs != NAND. Backupmenu backs up (presumably) rootfs, but not the kernel, not NOLO, not oops partition, etc.
In order to apply settings/changes from one N900 to another N900 you could "easily" do it on the mirrored copies (i.e. with the advantage of a full Linux, full/big screen, full/big keyboard, fancy tools/scripts, etc.) and then just sync back.
I don't use backupmenu eithier. However I know people have reported that if you are not on the same KP version, you get a boot looping device.