As a consequence of several interesting questions posted on BGG, a new version of the living rules for the 1985 series is available at this link.
The procedures for Flak fire have been drastically rewritten and should now be much clearer and leave no space for interpretations, without changing the overall impact and power of AA defenses. In short, there are now three different types of Flak Fire:
Transit Flak Fire: Used when an enemy air mission traverses an airspace containing SAM installations.
On-Station Flak Fire: Used against enemy air missions affecting a whole area or without a ground target (Air Superiority, Interception, Wild Weasel).
Ingress Flak Fire: The most dangerous type, used against air missions having a specific ground target.