The current affs driver doesn't support Unix-style devices on Amiga partitions, which makes it impossible to use an Amiga partition as root. A future release may support an emulation of devices and other Unix special files, perhaps based on the umsdos filesystem already available (or you can always try to code the support yourself).
You can use affs disks as secondary partitions. The AmigaOS 2.0+ symbolic and hard links are used to emulate the similar Unix features (hard links work as expected; soft links outside of the same directory will not work as expected from both sides, because of the differing semantics of AmigaOS and Linux path names).