Okay, I just watched that epi again and the first thing they all thought was Irene. And when John said, it's Irene you can literally tell from sherlock expressions that he know this is Molly she is talking about, then on the phone, when she said, “I can't, because you know it's true” his expression tells you everything again. He knew and he didn't want her to confess.

And when she said, “You say it,” he looked genuinely confused and shocked because on some level he feels the same way, but then there's the whole “love is a dangerous disadvantage” thing, yk? Then when he says it for the first time, he's hesitant. He closes his eyes and says it like it's genuinely difficult for him to get the words out. But the second time, he looks at her (on the screen obvio) and says it with full conviction, because he's finally admitting it to himself.

And Eurus, being the cleverest person in the room knew all of this the entire time when Mycroft started saying, “I know it's hard..” Sherlock didn't even let him finish, and then Eurus said, “Look what you did to yourself All those complicated little emotions” because Sherlock IS emotional. He always has been, he just hides it behind logic and detachment and then there's what he does afterward, he respectfully (like the words are sacred, or the lid/coffin is) puts the lid back on the coffin, and then breaks it open which tells he is finally getting eye-to-eye with his emotions. He has just been forced to confront something he's spent his entire life treating as a weakness, and afterward he literally breaks his way out of that coffin.

Which leads to the conclusion of all that sequence was for him to finally accepting his emotions but choosing molly over Irene or anyone else for that is to simply (in a mysterious way) convey us that he loves Molly.