Just spotted this thread and I would like commend you for starting this project. It's something I would be very interested in using.

Regarding the udev discussions, in case you weren't already aware (it hasn't been mentioned in this thread), udev was forked by the Gentoo guys as eudev with one of the objectives being to reintroduce support for a separate /usr.

A possible solution to get rid the optify mess could be to use a union file system like aufs or OverlayFS over the top of the NAND flash to ensure that further writes to will be written to eMMC flash.