This also appears to be affecting transparent areas on only some models. In my texture pack I have removed all the Squidward noses (sorry, not a fan), my Villagers and Wandering Traders appear normal but Iron Golems and all Illagers have the removed noses substituted back on as white blocks. This phenomenon appears black with default textures and white with imported Resource Packs.
Ah, I was hoping this had "fixed" it's self with one of the updates since it was reported, but also nice to see I'm not the only one 🙂
I found a work-around. Delete the Phantom_eyes PNG and replace with the Enderdragon_eyes PNG (renamed of course). You can then edit the new PNG in size and content and it will retain it's transparency. The only difference between the two files that I can see is that the Dragon_eyes is Indexed and the Phantom_eyes are not.