UnrealBloomPass does not support transparent backgrounds since the result is incorrect. The bloom does not blend correctly with the HTML and there is no way to fix this with the current approach of the pass. I also think that it is in general not possible to fix it since you have no access in WebGL to whatever is behind the canvas.
I have provided a version of UnrealBloomPass that supports transparent backgrounds to demonstrate the above limitation. Feel free to use it if you need some sort of bloom effect at any cost. You find the code in the below issue. But please keep in mind that the results looks different (buggy) compared to non-alpha version:
The issue also explains why transparent HTML backgrounds with additively blended post processing effects are problematic.