Actually, this has nothing to do with rally points. You could move the short-range ship directly there at any time. (So rally points follow a very simple rule: "anywhere your ship could go".)
The game rule is: You can always click (to set a ship's destination) within your own ZOC. Any ship, regardless of range, can go to anywhere in your (disjoint) ZOCs. They can cross any void to do it (but you're at the mercy of the path generator). You lose fine control over their direction while they're crossing a void outside all of your ZOCs (but you can make gross direction changes by rerouting them to a different ZOC, including back home).
That's GC3's chosen abstraction. We loves to exploit it, as befits a 4X.