This is just my opinion, not confirmed officially by Stardock, but from what I've gleaned from various sources, I don't think the Metaverse cares if you modified the game or not.
It appears that Stardock's design goal is not to disallow modded games, but rather that if you do modify the starting conditions, the AI is smart enough to make use of your modification as well, thus levelling the playing field between the player and the AI.
And as AIs get the same events you do, if you create a super duper colonization event that gives you PQ +100%, rest assured you've opened the door for the AI getting that event as well.
I think it's the better way to go. What's the point in putting so much of the game data in easy to read text files and then trying to stuff the genie back in the bottle by outlawing certain modding activities? No, Stardock has it right, provide the information, and then provide an AI which can fully take advantage of whatever *cheat* the player can come up with.