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H.264 does not support alpha channels. Use QuickTime Prores 4444 as your export format.
I'm not familiar with Unity but if it needs an Alpha channel QuickTime then Prores 4444 is the one to use.
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Alternative, you can use QuickTime Animation.
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I though Animation might be a possibility but can't find it as an export option (on Mac), maybe still available on PC from Premiere Pro? Though Animation is limited to 8bit.