Most definitely; in fact there are four new game modes (i.e., victory conditions) plus a revised Diplomatic Victory mode. The new modes include Last Flagship Standing, Last Capital Planet Standing, Research Victory and Occupation Victory. These can be toggled on/off during game setup.
When I was going over mods, I recall something about Flagships. Perhas the Last Flagship Standing is homage to that? Probably not,but maybe I just like to be a contrarian.
Also, I agree that we should have more options in game to tweak game settings. For example, I've heard on this forum of people playing "no cap ship" or "cap ships only" games. I know this has nothing to do with modders, but it would be cool if they plugged in some of those settings in.
Lastly, since for the past 10 years I've been a console guy mostly, all I think about when someone talks about modding is Warthog Racing above maps on Halo 2... that was fun.