Yes! I have done this successfully last night although it took me forever.
My BPI-M3 had Android in eMMC and working (somewhat), and I was able to boot using a microsd with Ubuntu and then reflash eMMC with Ubuntu image (I didn't dd from my microsd but used a separate image using USB drive).
Since then, BPI-M3 is running Ubuntu 15.10 (beta of course) using its eMMC. I didn't measure time, but it seems faster.
Now, I need its GPU driver, the whole source for M3 linux (whatever they want to call it since it's not going to be bananian according to bananian), and somewhat stability proved by SINOVOIP.