It seems to me that regardless of possible work-arounds here what we want from Cakewalk is an option to select a marker to determine where the end of project is. It would be good if you could have the situation that when you inserted the "end of project" marker a warning message appeared that said - " Warning all data will be deleted beyond this point - do you wish to continue?" That way any Meter/key changes, envelope nodes, tempo changes, midi data, data in archived tracks, data in hidden tracks, data in hidden busses, audio data imported at the wrong time stamp etc. would be removed.
You would obviously also need an option to remove the "end of project" marker in case you wished to extend the project. With this as well you could use it inconjuction with the in "end of project" marker solely to remove the unwanted data on your problem projects that played beyond your end of song.