I’m really not sure about the beacons. First off, there can often be a noticeable delay between the beacon ending and the spawn arriving; this can make it look like nothing happened. Second, as noted, the orange beacon doesn’t always yield an underboss.
I had wondered if there was some restriction on the type of underboss with planet faction, so if RNG rolled Franco Firewall but Maliwan types couldn’t be on that map you’d get a random replacement. However, it’s hard to read any consistent behaviour across multiple planets and maps when you have a dozen red dots swarming around you.