1. Create an alloy project with basic assets for backgrounds, buttons etc.
2. Create a new theme, copy assets over and replace images with alt. versions but keep the same filenames
3. Specify the new theme in the config.json
4. Build the project
Images are not replaced based on the theme - they remain as the original images however if you change the theme image filenames, then add TSS overrides in the theme to point to the new image, the theme is applied.
This didn't happen in 1.2 - if you replaced the images and did nothing else, the replacement images (with the same filenames) would be used.