Glad to hear it was useful! 
See this thread for some explanations/discussion on how the .rtf ToC is constructed – and maybe discuss the .rtf specifics further there, if needed, to make the forum easier to search.
I don’t have any experience to share, since I only really use .rtf for document annotations with many links. In that case I find .rtf more readable in the inspector, since you can hide the urls (the annotation inspector only shows raw markdown).
But yes, the ToC should be easier to manage with markdown, which has inherent structure.
You can also just convert your .rtf files in DEVONthink? (Right click > Convert > to Markdown), but I don’t know if it’s any better or worse than PanWriter (never heard of it). I was about to suggest PanDoc, but I see that’s what PanWriter uses…