In Indesign, I know the accepted way of creating 3 pages (back, spine, front) for a spread that will be used as a paperback cover. I use a 5 mm bleed as well.
The confusion arises when I have to work on a hardback, which needs the regular bleed for the jacket, but a bigger bleed for the pasted cover (the bleed will actually fold behind the endpaper).
What is your suggested workflow for this? Do I create separate files for jacket and cover? Most of my covers have the same design as the jacket.