This seems indeed quite necessary. I did the track rounding on a few PCB’s just for fun and it does seem to work quite good, but it does make later edits more difficult. In general I’m more with the path of least resistance here, and therefore I’m not likely to do this on real PCB’s.
One way to keep them separated is to just make a copy of the .kicad_pcb file and only round the tracks on that copy. A similar way is to first open the PCB directly in the Pcb Editor in Standaloe Mode, then experiment with the rounding, and use File / Save As to save the version with rounded corners to a separate file.