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I took this part: God's mercy has no limits, if He is approached with a sincere and repentant heart," to mean that if an atheist comes to God with a sincere and repentant heart, he will also be saved. To come to God with a sincere and repentant heart requires belief in God, i.e., an end to atheism for that individual. But that's just my opinion.

But that was not the premise of the question:

Francis recalled Scalfari had asked him whether God forgave those "who do not believe and do not seek to believe".

We're talking here about the hypothetical atheist that claims a clean conscience. The proper response to such a person would be to tell them that because of their sin nature, their conscience is not always reliable. Presumably, if an atheist approached the good Pontiff and asked him if there was anything wrong with his "clean conscience atheism", the Pontiff would have to say "no, nothing wrong with that at all. God will honor that with his boundless mercy".

Those who do not seek to believe should not even be asking if God forgives them. To ask implies that they are seeking to believe. His Excellency, the Pope, kind of ducked the question and answered from another angle, IMO.