I'd take the Reaching the Zenith briefing to mean that all of the active fighters and bombers in the theater of operations (or perhaps more specifically, on the Bastion herself) were getting fitted with the new drives, or at least as many as had been fabricated at the present time. As the FS2 tech room pointed out, the miniaturization required for fighter-size intersystem drives made them prohibitively expensive to deploy on any but a few select wings/squadrons at any given time, based on the specific mission requirements. One can picture maintenance teams swapping a handful of drives on and off fighters if a particular mission required intersystem jumps. The situation with the Lucifer was obviously very much the exception, as it was do-or-die for the alliance, and so every last drive available would have been put into use as-needed with no concern for the cost.