Mal's chronological age is irrelevant. He spent a big part of his life fighting a war, and a big part if that commanding others. If he's not old in years, he is in life experience.
The fact that he refers to others as "son" or "boy" only emphasizes his war-weary attitude. I thought it was obvious.
Yea, Simon was 27 going on 18, and Mal was 31, going on 45
Yep, that's it.
As to the "son", he's just letting this man who in any other setting would be far above him in privilege and social standing know that's worth jack on his
ship. He lets Book know the same thing right from the start, that being a preacher is worth exactly nothing.