When backing up live system you may end with some additional runtime garbage in the image but it doesn't hurt, better keep the system quiet when backing up.
Well, no, even the stock initfs can boot from mmc but you need usb flasher to set the choice,
there is no menu and only first found ext2 partition is used. When I created bootmenu, initfs could boot only from mmcblk0p1 which was not very useful for running cloned system.
Later they added search_root_onmmc() which scans all mmc partitions for executable /sbin/init and first one is booted.