You are of course right, Liverpool could lose against Atalanta but I think Liverpool are the favourites. Atalanta has a fairly productive attack line and so far they have proven their abilities by scoring 12 goals in the group stage and 3 goals in the round of 16. Liverpool  have to be aware of the possibility of defeat, that's can make them fail to win a semifinal ticket. So it is not certain which of the two they will qualify for the semifinals.

Liverpool have 3 matches in the Premier League before the Europa League quarter-final match against Atalanta, so maybe this could also affect the team in the Europa League, especially if several players get injured before the match. I'm support Liverpool to win that ticket, but not underestimating Atalanta.