[MC-256749] Fully transparent textures are missing from the texture atlas leading to errors in custom block models

Fully transparent textures are missing from the texture atlas and cause errors in custom block models. My resource pack uses a completely transparent texture in some block models to create different variants, but in 22w42a all those blocks started rendering this texture as missing. And the logs show these messages:

20:46:43.528   Missing textures in model minecraft:birch_leaves#distance=2,persistent=true,waterlogged=false:
    minecraft:textures/atlas/blocks.png:minecraft:empty
20:46:43.528   Missing textures in model minecraft:jungle_leaves#distance=7,persistent=false,waterlogged=true:
    minecraft:textures/atlas/blocks.png:minecraft:empty
20:46:43.529   Missing textures in model minecraft:dead_bush#:
    minecraft:textures/atlas/blocks.png:minecraft:empty