All tabs in window are saved regardless of subnodes

Just started using TO and really loving the concept. But in trying to understand all of the rules and functionality I'm a little confused by the behavior I'm seeing.

In an attempt to understand how TO decides whether to save a tab or not, I'll open a window with several tabs, some of which I'll add notes to or "Close and Save". I then close this window through the Chrome close button in the top right corner, and all tabs appear to be saved, even though I only expect ones with notes in their subnodes to be saved. Not only this, but upon double-clicking the now greyed-out "Window" line in TO to reopen my tabs, the window duplicates all existing tabs (not notes) and opens them in a flat hierarchy.

I have made sure to disable the "Continue where you left off" option and have "Open the New Tab page" selected. I have also read this post and made sure that the "Fast tab/window close" flag is disabled. Am I just misunderstanding the way TO works, or is this a bug?

Thanks!