What TaoChaos said. In the Dreamcast and Gamecube versions, you can't go into the Ruins without all three pillars active. If I recall reading or watching somewhere, there's a barrier that prevents entrance to the Ruins (and a portal that takes you back to Pioneer 2 if you can't enter the Ruins), and it only disappears if all three pillars are activated. That location isn't present during normal gameplay in Blue Burst, so activating the towers isn't necessary (though still nice to do the first time around).
You still have to activate them in a few multiplayer Government quests as you progress through the storyline, though. One of the quests even takes you to the area outside of the Ruins so that you can check the transmitters there before starting the Ruins proper.