@Sebastian Dröge this gets me similar output to the crossfade-ratio on compositor when changing the alpha properties in an inverse relationship.  You need to ensure ensure the background is either black or transparent otherwise the background color will blend into the output.
g_object_set (red_comp_pad, "alpha", 0.0, "zorder", 1,
    "blend-function-src-rgb", GST_GL_VIDEO_MIXER_BLEND_FUNCTION_SRC_ALPHA,
    "blend-function-src-alpha", GST_GL_VIDEO_MIXER_BLEND_FUNCTION_ONE,
    "blend-function-dst-rgb", GST_GL_VIDEO_MIXER_BLEND_FUNCTION_ONE_MINUS_SRC_ALPHA,
    "blend-function-dst-alpha", GST_GL_VIDEO_MIXER_BLEND_FUNCTION_ONE, NULL);
g_object_set (green_comp_pad, "alpha", 1.0, "zorder", 0,
    "blend-function-src-rgb", GST_GL_VIDEO_MIXER_BLEND_FUNCTION_SRC_ALPHA,
    "blend-function-src-alpha", GST_GL_VIDEO_MIXER_BLEND_FUNCTION_ONE,
    "blend-function-dst-rgb", GST_GL_VIDEO_MIXER_BLEND_FUNCTION_ONE_MINUS_SRC_ALPHA,
    "blend-function-dst-alpha", GST_GL_VIDEO_MIXER_BLEND_FUNCTION_ONE, NULL);