The best choice and most pleasing to the eye is to case it out just like a window or picture frame. You might have to rip a 1/4 inch off of window casing since most casing is 2 & 1/4 inches.
First let's deal with the spacing. That's too bad the light is not exactly centered as this does present a trimming out problem. I suggest you look for something other than regular window casing (2 1/4) Try to find some molding that is only an inch and a half. This way all of the corner will align correctly when mitered and will give a better finished appearance. If you prefer to still use 2 & 1/4 casing then yes the ripped edges would go against the side of the shaft. There opposite edge would just overlap the skylight frame just enough to leave a quarter inch reveal. You should have no trouble nailing finish nails into this trim since there has to be framing around the entire skylight.
Please don't hesitate to ask more questions if you feel it necessary.
I understqnd the situation and I suggest you use a tube adhesive like "Liquid Nails" or similar. Once you have "dry fitted" your trim pieces run a bead of this adhesive the length of the piece and then use a minimum of very small finish nails to hold it in place.
PS ... I don't want to go to New Jersey as I'm afraid of the Sopranos.....
Well, which ever one it was should be whacked !!!! Good luck to you and I feel confident it's going to turn out alright.