I went back and read this over again, looking for holes and things I could pick apart to start a discussion with... and there just isn't much. I think this might be a case where you simply did a really good job of explaining things. The principles involved seem pretty clear, and I can't think of any real questions.
About the only thing I can see that might be worth chasing around is the idea that defining the theme is fairly subjective, because not everyone will "lock on" to the same thing in a given story.
For instance, when you describe Silence of the Lambs as a buddy movie, I can see where you get that. There is definitely some resemblance there, and it seems likely it was an intentional structure choice. But when I ask myself if that's really the theme, the One Big Thing that makes the movie what it is... I have to say, I really don't think so. It's not what I took from the movie, what's stuck with me all the years since I first saw it. To me, the theme of Silence of the Lambs is not, "Let's do a buddy movie about an FBI agent and a serial killer." To me, it's much more about exploring the idea of a genteel and charming, even weirdly likable, serial killer. It's all about the fascination of the horrific. His "buddy" Starling is merely our means of getting to know, and be charmed by, him (without making the film from Lecter's viewpoint, which would be a little too much of a gross-out), and the buddy movie structure is merely a means to an end - the end being to mess with our minds so much that it makes us like a cannibal, and that's scary as HELL.
So, tying things back to last week, I'd guess the movie is largely execution driven - it would have to be done as well as it was, to work at all. Could it have been done, as successfully, without being a structured like a buddy movie? Possibly. Could it have been done, as successfully, without that exploration of the charming, genteel side of the character? Not a chance. Without that aspect, Silence of the Lambs might as well have been any episode of Criminal Minds.
The choice of endings for Road to Perdition sounds similarly subjective (I haven't read the GN, so I'm going largely by what you've said here). The choice of a given theme could make the ending seem appropriate, or not so appropriate, depending on what someone else sees the theme to be. Someone who felt that the son consciously choosing to end the cycle of violence was an important thematic element might be disappointed to discover that choice taken away by the revised ending, reducing the son's freedom from a life of violence to a matter of luck rather than a life-long struggle. That seems like a pretty significant change. Is the change worthwhile? That probably depends on how you want to look at it.
This effect of different themes or different facets of the story seeming to dominate depending on which way you turn it and look at it, is the same effect that complicates my life when trying to come up with pitch hooks - in any given story, there's often more than one candidate for the position of "primary" theme (sometimes a few more). And choosing "the one" isn't always as obvious as it sounds. I'm sure it's even harder in an adaptation, where whatever choice you make is guaranteed to disappoint or tick off someone.
I imagine it all boils down to just making a choice, and hoping it's one that the majority of people can get behind. If you do it well enough, it's magic.
*Fans out a deck of cards* "Pick a theme, any theme."
*Pulls a card from behind your ear* "Is this your story?"
So, those are my thoughts. Are you sorry you asked for more discussion yet?