Yeah that "Godfather" shout out was intentional. Likewise so was the "Heat" reference in ep 5, when Hank mentions "Heat on Blu-Ray" then the same ep the new guy (Todd) murks a witness during the heist which leads to more problems. That's the exact same plot as "Heat".
On a side note: dunno if you noticed but the book of poetry first popped up in season 3, ep 5 "Sunset":
It was after this scene:
Also the book of poetry popped up a few times this season, but most people didn't notice:
Lastly, this ep had a few shout outs to previous seasons. The scene at the end with his fam is an exact mirror of season 2, ep 1:
The paper towel dispenser is a shout out to season 2, ep 9:
Walt uses the same line on Lydia as Mike used on him in season 4, ep 2: "Learn to take yes for an answer".
Lydia uses the same line on Walt as Tuco used on him in season 1, ep 7: “We’re going to make a LOT of money together.”
The painting in the scene with the neo-Nazis was in season 2, ep 3:
etc etc etc. Lots more stuff too.