Is there any single-board computer/system-on-a-chip with good documentation for developing bare metal?
At least the NXP i.MX6 has most of the documentation publicly available (except for the GPU). There are many development boards (SABRE, Boundary Devices, Novena or systems-on-module for this SoC (check for example Variscite).

Check out also the "big" SAM line from Microchip.