Just as the title says, packing two images with the same name but different paths will omit one of them.

For example, adding the following two PNGs individually to the pack files list:

same_name_but_different_textures
├── same_name.png
└── subdir
    └── same_name.png

and then packing them, will omit one of the images in the emitted atlas. I expected a warning or an error but that was not the case.

Archive used in the example above: same_name_but_different_textures.zip