I've never had any issues with adding WSE2 launcher as a non-steam game, it always keeps my steam overlay when I launch it...just gotta be sure to launch it from steam. In fact on WSE and WSE2, since cRPG stopped working through Steam's warband, I've ran it through the steam overlay.
In steam under library, click games, add a non-steam game, and then browse to the WSE launcher in cRPG folder