The 2.00.03 patch (download link) is the final patch for the 2009 UCCE 2.0 game. It will install over any previous UCCE 2.0 version regardless of where it was purchased.
It advised that you apply it to a new install of the 2.0 version (2009) of the game.
No further patches will be released for this 2009 legacy product. So, consider this as a gift for your support. :)
All future updates are only for The Lyrius Conflict DLC which only works with the Steam version of UCCE 2.0.
If you have the paid version of the 2009 UCCE 2.0 game, you don't need to buy The Lyrius Conflict if you only want this final 2.00.03 patch.
PATCH 2.00.03
This patch does the following to a new or pre-existing UCCE 2.00.XX install
NOTE: If you installed the full game in your Steam folder so you could run it from Steam, then the patch should work I think. I can't guarantee it though; so you're on your own. You just need to point the patch to the install folder when prompted.