In Java it is replaced with solid black (which this mod also does), but in Bedrock it isn't.
Which is why some skins on sites like PlanetMineCraft utilize it to make more.. interesting skins.
So I think there should be some way to load such skins and keep the transparency, maybe again as a config.

Examples of skins with transparency:
https://www.planetminecraft.com/skin/small-creeper-6310610/
https://www.planetminecraft.com/skin/deadly-ghost-5497924/