IS this a mod for Birth of the Federation 2, or is this something different all together?

Yeah, I'm really new... I didn't see any links to this as a separate game (yet) so I created a new topic to find out. So has this been released if it's a different game? I couldn't find a place to download it, and I browsed the site" http://www.botf2.com/bote/default.aspx.

If someone could direct me that'd be great.. thanks!

It is a different game originally starting as a second botf2 project aiming at the same goals as Supremacy here but later on deciding to remove Star Trek and continue with a self-made universe. You can download this stand-alone game (it's no mod of anything) at http://www.star-trek-games.com (the main portal page of this forum here) after logging in / registering.
You might find it worth to read through the announcement threads in this subforum a while for more information about the game. It has nearly all gameplay features known from good old botf already implemented and is very playable and hopefully fun to play.

The other site you linked is just our resource page where we store game data and development tools and stuff.