there is no difference between a program and an app
Yeah the naming is confusing. The reason is what you said - machine vs app.
Back on Windows 9x, some apps would store files directly in the C:\Program Files directory. This was 'fine' at the time since every app ran with full permissions. Users were at C:\Windows\Users, but users were optional so not every install used it.
Windows XP had a better NT-based permission model (not nearly as improved as Vista, but better than 9x) and allowing regular users to write to the Program Files and Windows folders wasn't really a good idea. It added two directories for settings:
C:\Documents and Settings\username\Application Data for user-specific data
C:\Documents and Settings\All Users\Application Data for non-user-specific data
Vista kept the former but moved the latter to C:\ProgramData. I can't remember why.