Just sharing my experience on this.
Based on heavily modified instructions from this thread, I managed to get this running on PR1.3, works with BackupMenu & Bootmenu (no both of them are not evil), & even have multiboot for the system in NAND & the system in eMMC. Even managed to upgrade the kernel *after* setting this up, either on the NAND system or eMMC system first (;note that both must at least have kernel-power & kernel-power-modules installed if you wanna install kp). My set up has an instance of optfs for NAND rootfs & eMMC rootfs each. Only thing I couldn't & didn't bother to fix was that it would boot up automatically again after a shutdown.

So, I basically ran rootfs on eMMC system for 2 days (used a current image created using BackupMenu), & I gave up. It was horrendously slow (boot up that usually took 1 minute or less on NAND took perhaps 5-10 minutes). I find that it sucked up more battery too (perhaps it kept the hardware up for longer time due to longer read/writes, & I have quite a bit of background processes running on mine). The main battery drain on my N900 was 24x7 online 2G which on NAND, can stay up for about 12 hours max without charging. With rootfs on eMMC, there wasn't any noticable battery savings.

Perhaps it was just not meant for my circumstance, where I have lots loading/writing from/to the file system & apps in memory.
A set up of rootfs on eMMC using a freshly flashed image was actually not too bad, provided one continues keeping things minimal in the device. I suspect the set up I made could stay quite stable if my eMMC rootfs wasn't created from image of my NAND rootfs.

Conclusion: Something I wouldn't go on anymore. But might be suited for folks who really scrutinize everything that goes into their device & keep things minimal. Not for those not familiar with technical stuff too.

I can share some of the work I did if anyone wants, but would expect whoever wants it to be able to figure out stuff on his/her own & reverse engineer things as well. Won't be actively providing help.

kh