I have no idea how you might go about changing that setting on a per-post basis. You might be able to “fake” the flat layout by using some CSS styles to undo the indenting and then hide the “Reply” links on each comment; that would essentially give you a flat layout even while comment threading is enabled. You could then write some code that only applies those “flat CSS rules” when a post has a specific Custom Field.

You might try posting your question in the WordPress.org Support Forums to see if anyone else has any suggestions.