Not sure if this is what you mean, but we typically keep the majority of our images in folder outside the platform folders and then generate sprite sheets as a build step with a small gradle task and it works quite well.
Here's an example project: Ludum Dare 46
This way you just have to remember to regenerate the sprite sheets if the source images change at all (the gradle task can be added as a pre-launch step to one of the run configurations in the IDE if you want it done every time, but if nothing changes then there's no need to run it).
Check the following spots for details:
- /sprites - source folder for sprite images to be packed
- /desktop/build.gradle - sprites task
- /core/assets/images/.gitignore - so we don't version control the generated sprite sheets
We do keep some other stuff directly in the assets folder, specifically title screen images and other large images that won't fit in the sprite sheets, or images that we know we need to load as actual Texture objects (not TextureRegions) because we need to have custom texture wrapping on them or they need to be used in a shader in a way where neighboring pixels in the sprite sheet would cause problems, etc...