High praise indeed, thank you so much for sharing! I'm really happy to hear that a lot of the small touches have made things smoother and easier for you.

And you're right about modifying the bookmark folder itself—not only should there be no detrimental effects, it is fully-supported to move bookmarks around however you please using the tool of your choice. (Extensions that auto-move bookmarks do sometimes cause problems, but this is the exception, not the rule.)