Most popular modern SoCs are not fully documented - one part that usually lacks any documentation is the GPU. For most ARM-based SoCs, it's either one of ARM's Mali series or an Imagination Technologies product, most RISC-V based SoCs (e.g. the JH7110) also use Imagination Technologies GPUs.
Additional components also have documentation that's hard to find, especially those based on Synopsys' DesignWare IP. These are sometimes at least... strange (or should I say buggy?) effects such as with their "standard" 16550-compatible UART: https://lupyuen.github.io/articles/plic
The Vivante GPU in Freescale's i.MX8 SoCs was reverse engineered and is probably the closest you can find to a somewhat documented GPU (STM32MP SoCs also have a Vivante GPU). In general, the i.MX8 is well documented - one of the reasons why it is used in Purism's Librem 5 phone.
You can "cheat" and improve the GPU situation a bit by using a RISC-V board with a PCIe slot and an old AMD GPU.
When there's no documentation available, all you can do is reverse engineer the functionality of existing open source drivers. Linux drivers are often quite complex, I recommend looking at Net/OpenBSD and Plan9 drivers instead. For some RISC-V SoCs (SiFive Freedom U740 on the Unmatched board and JH7110), Haiku is also worth looking at.
An alternative which provides documented hardware is to use an FPGA-based SoC builder, e.g. LiteX: https://github.com/enjoy-digital/litex
Of course, this results in a significant degradation of performance...
Another option would be to use a regular x86-based PC and rely on the documented interfaces, such as VESA graphics, but then you have to deal with x86 and all the baggage of almost 45 years of PC evolution...