We recommend that you start by creating the latest version of libvpx itself on a 64-bit Linux workstation. The libvpx test suite should include a test for the alpha channel. Make sure the test passes. If this is not the case, this is a bad sign, because libvpx is the reference implementation for VP9.
If this happens, the next step will be to attempt alpha decoding and overlay using a higher-level library still located on Linux. I suggest using GStreamer 1.8.2 or higher. Put your clip on top of the videotestsrc generator, which will generate most video formats.
If any of these tests failed, I would recommend that you carefully study the reason before proceeding.
The reason for starting Linux is that you will have an easier time to create and troubleshoot, and I suspect that you may run into the edge of a specification that was not even implemented in the reference implementation (libvpx), or which is difficult to integrate into libraries more high level (hence the proposal of GStreamer).
However, although I have extensive experience with VP8 and libvpx, I have not used the feature set specific to VP9. However, I am curious to follow your efforts and perhaps you will be able to give advice as you move forward.
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