I know that the site put up a disclaimer about 2016 data not being up to date, but the 2012 data is definitely not right. For example I noticed that this app had Riverside CA going to Romney 290,227 over Obama 287,754 with Johnson+other at 11,740. The Atlas has Obama 329,063 over Romney 318,127 with other at 15,926. That's a substantial difference.
I looked at a few other counties and the app had lower vote counts than Atlas. I suspect the vote totals on the app come from a media source that quit updating late on election night or shortly thereafter. That would leave out all the late absentee and provisional ballots that are included in the official Atlas count.
I noticed the same thing, especially looking at California. It's fun to play around with, but it's not really usable until it has the finalized election results for every state.