I think I fixed this with e21debbf751c86a991dc1fdc39bc4e3b7b82b9cb ("glcpp: Don't define macros for extensions that aren't in ES") almost a year ago to the day.

git tag --contains=... says that it's in

mesa-9.1
mesa-9.1-rc1
mesa-9.1-rc2
mesa-9.1.1
mesa-9.1.2
mesa-9.1.3
mesa-9.1.4
mesa-9.1.5
mesa-9.1.6
mesa-9.1.7
mesa-9.2
mesa-9.2-rc1
mesa-9.2-rc2
mesa-9.2.1
mesa-9.2.2
mesa-9.2.3

and I can't reproduce with a shader_test:

[require]
GL ES >= 3.0
GLSL ES >= 3.0
[vertex shader passthrough]
[fragment shader]
#version 300 es
#ifdef GL_ARB_draw_instanced
#extension GL_ARB_draw_instanced : require
#endif
void main() {}

but I suppose there could be a bad interaction caused when creating the shader program via GL_ARB_ES3_compatibility?

m.b. it's because of versioned context, I create context like this:

    int attribs[] =
    {
        GLX_CONTEXT_MAJOR_VERSION_ARB, 3,
        GLX_CONTEXT_MINOR_VERSION_ARB, 1,
        GLX_RENDER_TYPE, GLX_RGBA_TYPE,
        GLX_CONTEXT_PROFILE_MASK_ARB, GLX_CONTEXT_CORE_PROFILE_BIT_ARB,
        None
    };

    glXCreateContextAttribsARB(..., attribs);

Patch sent to the mailing list (and with you Cc'd). Please test! :)

(In reply to comment #3)
> Patch sent to the mailing list (and with you Cc'd). Please test! :)

I've committed the patch. Feel free to update this bug report if you test it.

Didn't have time to test it, I'll try it today, thanks!