Update: with 10.11.4 final I get no artifacts on the integrated graphics. Yay! (However, the update broke audio so I will need to try re-installing the driver from MultiBeast.)
Also, the framebuffer usage changed, meaning that my HDMI 4K display is only recognized as a 1080P TV. I need to come up with a Clover patch to reset the correct entry to the HDMI connector type, and hopefully that will take care of it (the previous patch doesn't fix it any more).