It is really not possible to know what the designers of Starcraft had in mind when they decided to include the special victory conditions as part of the game. My guess though would be that they wanted to ensure the game would end in a relatively reasonable time. If you are not familar with Christian T. Petersen, he is the designer of the somewhat infamous galactic conquest game Twilight Imperium. I have never played this game, so I really cannot comment too much on it, but the one thing that is always attached to this game is that it takes forever to play. From what I have heard the typical game will last 6 to 8 hours. I am pretty sure that Christian did not want this to happen with Starcraft the board game. With a 3 player Starcraft game, one can expect that a special victory condition will end the game in about 2 to 3 hours. But I still have to ask the question, are special victory conditions necessary?
Back in my first strategy article I wrote about the different special victory conditions of each faction. I asked two questions. 1)Could the special victory condition be achieved by conquering two full planets? 2)Could the special victory condition be achieved by capturing two full planets and a beachhead on a third planet. Some of the factions answered yes to the first question, but all of the factions could answer yes to the second question. As a result, it seems that players just need to section off a couple of planets and simply hold onto them until Stage 3 of the game rolls around. While Starcraft favors aggressive players in a lot of ways, a player only needs to be aggressive to a certain point to win a battle.
That is why I suggest you try a simple solution. Get rid of the special victory conditions. Instead just play for conquest points. This will always force at least one player to be on the offensive as sitting in your own corner of the galaxy will not help you win the game. To be honest, I have only played one game like this, but it was our best game. Each player fought for every conquest point they could get and the game was neck and neck all the way to the end. To end the game, either a player must earn a specific amount of conquest points or two End Draws Near cards must turn over and the player with the most conquest points at that time will win. Therefore, the game will still end in a somewhat reasonable time.