>>7606415One could see it as progression from a large, well-organized and established empire to a smaller, scattered outfit still in recovery mode after the Space Police cracked down on their original setup. Having a large conspicuous base probably made the SP's job easier once they were ready to take them down; BL2 have learned from this and switched to smaller outposts for coordinating their raids.
Decentralization and low visibility are key for factions based around the spying on and raiding of others, Spyrius demonstrated this with their own base being partially disguised as a rock formation. In the case of the BL2 base, I bet the lights are part of their electronic warfare systems, probably for jamming hostile scanners to help conceal the base from prying eyes. Even so, BL2 seem oblivious to how conspicuous those those big trans-neon green panels are, unless the intention there is intimidation and deterrence.