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I think this repo explicitly wasn't designed to handle transparency. RGBA colors (unorm8_t) are converted to RGB (vec3) internally during the compression process, even in places where transparency would be easy (e.g. void blocks). I'm a little unsure why they do this- it was easier to write, maybe?
However, this repo from typed seems to fix the problem! It's pretty much a drag and drop replacement for the astc/ folder (though it's in CPP instead of CC and you do have to change some #ifdefs). Simply enable alpha by adding a true parameter to the end of compress_texture and it should work.
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