Real Madrid showed that they are always stronger in the Champions League than in any other competition. I accept that the point gap is only a point difference, but Madrid still has a better advantage of qualifying to the the next round than Atletico. We might see a different game in the second leg, and Atletico performance might not be good enough to stretch the game to penalty shootout.
I also don't think that Real Madrid will give up in the second leg because Real Madrid usually can also put more pressure on the opposing team in the Champions League when they are in such a crucial round. So in the second leg there is a possibility that Atletico will feel much greater resistance from the team that has held 15 UCL trophies until now even though most people also admit about Atletico Madrid's greatness in La Liga this season, but when talking about the Champions League, this will be very different for any team.