I'm confused by this latest post. In your commentary you state that you have concluded that it is no longer to have chapter or section number on a line by itself.
I agree with you for the reasons you stated. Therefore, I don't understand the conclusion that you apparently reached, that sample #2 is the better choice. Sample #2 does indeed put the section number on a line by itself and I think the result is not particularly desirable. I would go with Sample #1.