It's worth being clear that there's nothing technologically that clever about ProRes. It's very similar to basic motion-JPEG, which was used from the very dawn of computer editing. Many of the things which are attributed to it can be done with many other codecs.
This issue of files coming in complicated folder structures is and always was craziness. It's completely unnecessary, it's enormously unhelpful and it's arguably misuse of a computer filesystem. When Panasonic came out with P2 I was horrified at how badly it had been done. Even MXF itself is a disaster; massively overcomplicated and so desperate to be everything to everyone it ended up being nothing to anyone.
It should always just have been file per take, just like Broadcast Wave.