I'm just as confused, especially as regards threads for quilting. I was watching one of Leah Day's videos yesterday and her advice is simple: always use the same thread, same colour, top and bottom. She uses a synthetic embroidery thread. Like you, Bottom Line puzzles me: using a much finer thread in the bobbin surely makes it more difficult to get the tension right? That's what I've always found, anyway. However - I hit on the idea of using Bottom Line top and bottom for stitch in the ditch, and that worked brilliantly - there's a good range of colours to choose from, and, being fine, the stitches didn't show on the top as much as they sometimes do. My machine won't take machine quilting thread, eg King Tut or YLI - it sticks in the tension discs - and does much better with a fine synthetic, eg Superior's Rainbows or Robison Anton embroidery thread (which Janome recommended to me).
I'll follow this discussion with interest!