My situation is like this:

I have lots of characters and they don't share the same export scale. e.g. 50%, 75%, 100% While "Pack Setting" page allow me to set different export scale, It is not good enough for the work flow. It takes more time to generate all scales and I only need one. Every time I exported, I have to manually go to the folder and delete those I don't need. Otherwise Unity will detect and process those new files which will further slow things down.

Ideal case:
I set a scale to a project instead of to the application. Each project export with their own scale setting.
So that I can just press and export button to update file to the game without further delete file action.

What I am asking is something like adding a check box "Override/Custom Pack Setting" to save the pack settings to current project instead of sharing between projects.

Yes. I have multiple Spine projects files. They do not refer to the same image folder.
Yes. I have some packing setting requirement for different projects. e.g. some characters use 75%, 100%, scene use 50%. something like that.
The problem is that current packing setting is shared between projects. If I change one, it will affect all other in unrelated projects.
Yes. The export folder is located inside my unity project because I am lazy.

If the answer is no you could avoid exporting the atlas files and just update the json/skel file.
Do you mean I just uncheck the "create atlast" option and it will only update the animation? Sounds like a good idea! Didn't realize I can do this. Thanks.

But still, it is better to have project remember my export scale in case I need to update the sprites and recreate the spritesheet.
When handling different projects, I generally need to export with different scale. "Set it once and forget it" is still a better approach in my opinion.
Don't you think export scale should be a project setting instead of application setting?

Oh. Just read that last post.I guess this will do.
Thanks