What's the difference between a flat fee per filing and a fee per application per year?

A per-filing fee prices the document: the application is drafted and filed, and later work is a new engagement. A per-application-per-year fee prices the journey: the same fee covers the filing year and the years in examination, until a decision on grant. Since most applications receive at least one office action and USPTO examination typically takes 2 to 3 years, the difference decides who pays for prosecution.