Oh, compiling them together is no problem. It's just that there are some conflicts when using them. Just to be clear which driver supports what:
The rpi SDL video driver was written back in 2013 for the old firmware-side driver. It will only ever be relevant for that driver and I'm sure the readme will be updated eventually to reflect that. X11 was never really a thing here. The libsdl2 package in the Raspbian repository was compiled without it.
The new driver can be accessed with the x11 SDL video driver, both of which you seem to be already using... or trying to use. Still working on the issue with your OpenGL calls.
I don't think that the new SDL version will cause any issues for you. The new Debian Stable version "Stretch" that was just released apparently has SDL 2.0.5 in it. If you think the package should be handled differently, you would have to contact the maintainer of the package and explain the issue. This being Debian, I doubt you could convince them to change anything now unless there's some huge issue with the software. No idea when Raspbian will switch to Stretch, though.