If you watch one of the KH2:FM+'s new curscenes, Xemnas explains that Axel's sacrifice triggered Roxas to come out...
"Tell me why he picked you"
Most people believe that it had something to do with DiZ, and how he chose Sora to take down Organization XIII, instead of Roxas.
Although in recent light of events, it may also have something to do with Axel, but that's just a theory...
"I see, that's why"
Prior to this, Sora thought Roxas was Riku. When Roxas saw the stained glass floor, he knew why Sora asked him that, seeing that Riku is Sora's friend.
It's also possible that Roxas was referring to Riku, who chose to get back Sora rather than let Roxas stay as he was, and his line "I see, that's why" would mean he understood why: Riku was Sora's friend.