Hi, sorry for the late response, but I wasn't sure this fit.
ERROR: device 'r' not found. Skipping fsck. ERROR: Unable to find root device 'r'.
You seem more knowledgeable than me about this, but I found a similar problem in Gentoo whose responses may be of use: https://firstname.lastname@example.org/msg157987.html
In there, too, often I find that mounting manually works, it doesn't find the root device right automatically.
Although the problems are different, they might have a similar solution. Maybe you should try the suggestion of creating your initramfs manually?
Hope this helps, João Miguel