Dear Samuel, I like the way you frame the issue and the solution you are sketching.
I am not fund of a "dedicated top-level entry for all file-level control purposes" because it transforms the ambiguity about keywords' scope into an ambiguity about structure: IMHO a subtree should never be something that you always want to remove when exporting. But allowing a top-level :PROPERTIES: drawer with properties whose scope is the entire file looks like a good idea to me. How other would feel about this? -- Bastien