My experience with using WRClient is based on Shift, not Shift2. With Shift, the reason I installed to my second OS, is that when the game is only copied into a new folder in the same OS, the savegame files are directed to the same location.
I imagine that the same is true with Shift2. Meaning that if one wanted to segregate the savegame files, it would require that those files be backed up/restored each time one switched from the unmodded to the modded install (if one is in fact using the WRClient to record lap at http://wrecord.com/
I could have created a batch file to automate the backup/restore process, but since I use both OSs (WinXP & Vista), it's no problem for me to simply reboot the PC into the approprite OS.
Otherwise, it probably doesn't matter to most users which savegame files are most current, and your solution is probably the easiest for them.