"Finally, you're required to submit the project file (probably winners only) which may reveal to YoYo Games if the project has been worked for longer."
Firstly, submitting previously made games is within the rules. It doesn't matter whether yoyo sees the project date being older than the jam as they're not breaking the rules. No one is saying this is against the rules, just that it's against the spirit.
There are multiple completed games that are months old and have been reskinned and rejiggered a bit to work in the theme. That's a lot less work than making a completed game from scratch AND it yields a much more polished result (said games could have been in production for years previously). While they're not breaking the rules, I feel as pixel-team does, this negates any hard work done by people who were actually working within the time constraint imposed by the announcement of the jam (though not the rules).
In my opinion, the point of game jams is to showcase the creativity and talent required to actually make something from scratch within the jam period (with all the corner-cutting and creative solutions that entails), rather than simply to be a place to park games you've made before.