I'm sorta confused why "systems cut off" should be an issue for the A. I.
Unless I'm missing something, which I may well be, at this point in the game, and indeed realistically most of the game*, number of systems in an arm is pretty much directly proportional to the number of exploration ships exploring that particular arm. If they are cut off from an arm that has a number of systems but none yet of interest to them, they can simply redouble their efforts to uncover territory down the arms they do control.
*Granted maybe with the increased functionality in C# positioning yourself for late-game when the galaxy is well explored may be a more legitimate concern, IDK.