The final Garrett "scene " -- that seemed a bit out of context. I think that was just in either his head or Colson's head.
- It just doesn't make sense that they would have just left him there alone in the box for enough time that he could climb out.
- When Colson blows him away he is not wearing the suit jacket
- It goes directly to Colson on the plane (wearing the suit jacket) and yelling at Fury about the mind-altering affects of the drug.
Not being a Whedon aficionado, I didn't get the last scene with Garrett on the table getting all Darth Vader'd up and then blowing up. It makes sense as an internal dream of Garrett. He was dead for sure in that box and I was kind of hoping he'd survive to come back and cause more trouble. But I guess there's lots more villains in the Marvel universe.
It is a classic Whedon move that doesn't need to be over-analyzed. It's the subversion of a trope, mostly played for laughs, but also to close the book on bringing back the bad guy. Think of Loki getting ragdolled by the Hulk in The Avengers, as far as the humor.