Well, that is a philosophical question. And the best answer depends on your goals. You are putting the export files on a blue ray. Interlaced display technology is outdated. It is almost certain that any device you choose to play your files on will be a progressive display device. So maybe the question should be: why would you want the output to be interlaced?
There is a related topic here where I recommend to deinterlace and upscale NTSC source clips to get the best export quality. This is just my opinion, but I have been happy with the results in the past:
I agree with your previous assumption - some metadata must have been lost through the conversions.
That was going to be my next suggestion. I am glad you were able to figure that out.
Well, Shotcut doesn’t really know that you are replacing a clip with a surrogate clip that is exactly the same content. If we changed the behavior to map over the cut points, then someone else would complain about the behavior when they want to replace a clip with a completely different clip. We could add more options… but I think the XML edit is a pretty good solution in this use case.