Consider the default textures, and two separate texture packs in natural load order.


Default:
Texture: minecraft:textures/blocks/mipmaps/stone.png
Mipmaps: Files not present: Auto-generated
MCMeta: Since no mcmeta was found and the mips were auto generated do whatever MC does already.


Pack 1:
Texture: minecraft:textures/blocks/mipmaps/stone.png
Mipmap 1: minecraft:mipmaps/blocks/mipmaps/stone.1.png
Mipmap 2: minecraft:mipmaps/blocks/mipmaps/stone.2.png
Mipmap 3: minecraft:mipmaps/blocks/mipmaps/stone.3.png
Mipmap 4: minecraft:mipmaps/blocks/mipmaps/stone.4.png
MCMeta: Since no mcmeta was found then the virtual mcmeta is generated. There is more than enough information to determine that these are indeed mips and there is no need to generate them as it normally would.


Pack 2:
Texture: minecraft:textures/blocks/mipmaps/stone.1.png
Mipmaps: Files not present: Auto-generated
MCMeta: Since no mcmeta was found and the mips were auto generated do whatever MC does already.

Pack 4:
Texture: None.
Mipmap 3: minecraft:mipmaps/blocks/mipmaps/stone.3.png
MCMeta: Since no corresponding block or mcmeta was found then the virtual mcmeta is NOT generated.

Pack 5:
Texture: minecraft:textures/blocks/mipmaps/stone.png
Mipmap 1: minecraft:mipmaps/blocks/mipmaps/stone.1.png
Mipmap 2: minecraft:mipmaps/blocks/mipmaps/stone.2.png
Mipmap 3: minecraft:mipmaps/blocks/mipmaps/stone.3.png
Mipmap 4: minecraft:mipmaps/blocks/mipmaps/stone.4.png
MCMeta: minecraft:textures/blocks/mipmaps/stone.png.mcmeta


There is no collision between automatically generated and automatically loaded mipmaps.

The only REAL difference between how MC operates now is that a virtual MCMeta file is created if the mipmaps are available and no MCMeta file was found.