To be clear ... you are not using the WinClone app to change the partition size of bootcamp ... you are only changing the size of the Windows image within that partition to eliminate the "free space" for a smaller saved clone image. You use OS X BootCamp Assistant to actually alter the disk partition itself. And ... it is all done under OS X so there is no worry about a Windows utility screwing up your OS X disk.
WinClone simply eliminates the tedious process of re-installing Windows, the endless updates and reboots, re-installing all your Windows applications, the endless updates and reboots, and then re-activating everything again. Plus, you can keep periodic snapshot backups of the complete Windows environment using WinClone in the event you need to reinstall.