Yes but if you start with Ego Draconis the game continues into the Flames of Vengeance expansion as if it were part of the game all along. So you continue with the same character and same inventory and everythingCeebs said:The expansion is a separate item on the main menu.

And about the DRM "Issue" yes, you can deactivate it when you uninstall the game. The developers have expressed interest in removing the DRM further down the line, however.