This is expected. With autotools, the default configuration will not include the rpi video driver unless the host is specifically named as raspberry. This needs to be update eventually.
However, before that can happen the whole OpenGL library path situation has to be resolved or all other drivers fail to automatically load OpenGL if the rpi driver is included. Because this will affect almost all video drivers, I think that the solution to this problem requires something robust and reasonably well tested which means it’s probably too late for 2.0.6.
Perhaps it’s possible to find a maintainer for a special SDL2-rpi package in the Raspbian repositories.