Even moreso because Bartleby has become fully human and, for the first time, is able to experience a human conscience. So his apology really is genuine.
And the the rest of the ending's full of them.
Metatron's pep talk, telling Bethany about the time he had to tell Jesus about his true nature.
Bethany:[After finding out that she's the Last Scion and has to save the world from Bartleby and Loki] I don't want this. It's too big. Metatron: That's what Jesus said. Yeah, I had to tell him. You can imagine how that hurt the Father, not being able to tell the Son himself 'cause one word from his lips would destroy the boy's frail human form. So I had to deliver the news to a scared child who wanted nothing more than to play with other children; I had to tell this little boy that he was God's Only Son and it meant a lifetime of persecution and eventual crucifixion of the very people he'd come to enlighten and redeem. He begged me to take it all back, as if I could. He begged me to 'make it all not true'. And I'll tell you something I've never told anyone before: If I had the power, I would have.
Later in the conversation:
Metatron: You ARE Bethany Sloane. Nothing can ever take that away from you. Not even God.
Rufus' parting words to Jay and Silent Bob, before returning to heaven with The Voice, and God:
Rufus: And if ya clean up your language, I might just put in a good word for you guys. Silent Bob: Thanks.
In-universe example: Bethany initially thinks that it's sweet that Bartleby and Loki (who she didn't recognize) were stationed together before hooking up.
Another would be the beginning of the film, when we see that Bartleby enjoys visiting airports and watching the joyous reunions there. When Loki meets him, he points out a happy couple who are hugging and kissing. He says that the woman had an affair while the guy was away, but there they are, perfectly happy.
Jay and Silent Bob are under the false impression that Bethany is their girlfriend. At first it seems that they just want to screw her but it becomes clear that they do care for her. They steal the Cardinal's golf club as payback for him messing with her (which Bethany actually thinks is sweet) and at the end, when Bethany is dead, Silent Bob is weeping.
If you close you can see Jay shedding a few tears, too. Jay.