Subfolders normally cause the images in them to be output to a separate atlas page. Make sure
Combine subdirectories is unchecked and that you don't have a
pack.json file in your images folder that specifies
Are you saying that you do get your skin images from each subfolder on a separate atlas page, but the page number sometimes varies when you change/add/remove images? That is expected, as it wasn't a design goal for Spine's texture packing. It would be difficult or impossible to do reliably because when an image doesn't fit on existing pages a new page is added, which would increase the atlas page image file name numbers for subsequent atlas pages.
Why do you need this? Typically the file name of an atlas page image that a region ends up on is unimportant. If you need to know, you can programmatically get a region, get it's page, and look at the name.