After spending most of the day testing, I finally was able to render alpha channels correctly! Note: In my case this was only an issue while rendering to h.264 and h.265 .mp4 files. I rendered out to MPEG and Quicktime and other formats just fine. It was only with h.264 and h.265. Rendering using OpenCL, Metal, or "software only" didn't change the result. I tested other variable settings and the culprit appears to be the "Render at Maximum Depth" setting. If it is UNCHECKED it renders out correctly with the Alpha Channels working as they should. Hope this helps everyone!
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