Here's the answer from the developer; yes, you can do it, but you have to go to the command prompt and run it manually with the AppID as an argument: http://psteamcommunity.yuanyoumao.com/groups/idlemastery/discussions/0/610573009247516421/#c610573009251830844

Steam Achievement Manager can do this, easily and for multiple titles at the same time. You don't have to actually touch the achievement options. I used to use sam to idle for cards before I found this thing. Without cheating any of my achievements :v