If the "Fortress Republic" tech works in the manner that it appeared was being foreshadowed the Historical: War of 3039 sidebar on Black Boxes, Tucker Harwell's analysis, and the accounts of what happened to ships that tried to breach the Fortress: (Caveat - the new writing team certainly could have taken things in a completely new direction)
The source material established that hyperspace has a "high band" and a "low band." Pure energy, like HPG transmissions, uses the high band. Items with mass, like JumpShips, use the low band. The Black Boxes "ripple" the fabric of the high band - modulating it so that a receiver calibrated to monitor hyperspace can pick up coded messages. Scientists working on the early HPGs detected interference from Black Boxes (which were then cutting edge interstellar communication devices) and came up with adjustments to the HPG signal to compensate for the interference, which they recorded as chants. Tucker Harwell identified the problem with the Wyatt HPG as being hyperspace interference, and successfully recalibrated it (using the ancient chants - which were developed to deal with such interference) to transmit, suggesting that CLARION CALL was a weaponized black box variant technology that was causing the Blackout by "rippling" high band hyperspace and thereby blocking most HPG transmissions.
If CLARION CALL is a weaponized black box tech that can "ripple" the high band, it follows that the FORTRESS REPUBLIC is something that can "ripple" the low band, causing physical matter passing through to be fatally disrupted and spat back out. One of the Combine ships that failed to penetrate the Fortress looked like its physical substance had been realigned as though it were sand being pushed by a wave, with the bodies of the crew intermingled with the bulkheads. Rippled, in other words.
So, if the high band can be penetrated by energy by adjusting the settings to compensate for the interference...it follows that the K-F drives could be similarly tweaked to allow them to pass through rippled areas of low band. Or else, if you had one of the black boxes, you could transmit an inverse signal, cancelling out the FORTRESS signal in a localized area, and set your course through the calmed region. (Which is one way that Republic strike teams could have been getting in and out of the FORTRESS)
So, if FORTRESS technology becomes commonplace in the post-ilClan era, all you'd need is a scanner to analyze the local hyperspace for rippling, then set your device to counteract it, and it's back to business as usual. Not much different than the Listen-Kill Missile kerfuffle - a cutting edge weapon quickly neutralized as everyone installs countermeasures.
(Massive caveat - Cray's rulebook section on hyperspace flatly rules out "high band" and "low band" altogether, stating that ships simply "translate" from point A to point B without spending any time in hyperspace, which is not a place, but merely a mathematical construct. The new writing team may have gone with this interpretation and had the Fortress Republic interdiction zone enforced by Giant Space Hamsters, for all I know.)