...And just like that, naval combat was fixed forever.

Not even kidding, this is huge. Will these changes affect the AI's general eagerness to attempt a JP assault? I.e. no such thing as vast Swarms refusing to follow a slow, unarmed, commercial-engined survey ship through a jump point anymore?
If there is only one jump ship and the jump point is not stable, the fleet will use a standard transit.
This might be a minor nitpick, but could the entire fleet minus the jump squadron perform a standard jump, followed by the jump ship's squadron jump 5 seconds later? This would largely accomplish the same result, but also put a squadron's worth of combat-ready ships in the player's face while otherwise the entire NPR fleet will be defenseless until the long standard jump shock expires. Ditto for the many jumpships - unstable JP scenario, most squadrons can jump together with the standard transit group while the last squadron will follow 5 seconds later after enabling the transit, resulting in an extra combat-ready squadron on the field.
Also, have you considered taking a look at the Fire at Will command during JP assaults? Because I'm pretty sure there's still some
unfair player advantage to be had.