In the VJ community, QuickTime is still used heavily due to the HAP codec being decompressed on the GPU and includes support for an alpha channel.
After Effects still does not support exporting to the MKV container and so it doesn't fit into my typical rendering workflow. Hence I've stuck with MOV using HAP-alpha.
As a experiment, I rendered out a PNG frame sequence (with alpha) and then used FFMPEG to render out both an MOV and MKV using the hap_alpha codec.
--- When I tried importing both videos into Resolume then the MOV was successful but the MKV was rejected. Doesn't seem to be a supported.
--- VLC could not playback the MKV.
--- MPC-HC successfully played back the MKV and reported it was an rgba video.
So it was interesting experiment, but not something that my necessary software pipeline supports.
Here is some of my 3D animations for context. https://www.jasonfletcher.info/vjloops/