How about using the tracks as your organizing tool?
You can place a clip on one or more tracks at will, while still having only one file in the project; splitting clips to isolate the relevant parts is non-destructive, you could move them to aptly named tracks.
As for point 2, every split clip can have its own time stretch and pitch shift settings, without affecting the other selections from the same source clip, and that too is non-destructive, so you'd still have just one file in your project.
How about using the tracks as your organizing tool?
You can place a clip on one or more tracks at will, while still having only one file in the project; splitting clips to isolate the relevant parts is non-destructive, you could move them to aptly named tracks.
As for point 2, every split clip can have its own time stretch and pitch shift settings, without affecting the other selections from the same source clip, and that too is non-destructive, so you'd still have just one file in your project.