Windows and BeOS have very different behaviors when copying a folder to a location that already contains a folder of the same name. Both systems will offer a „Replace?“ dialog, but saying yes to this dialog in Windows will cause all new files to be added to the existing folder, while BeOS will overwrite the entire folder.
For example, if you drag a folder called „config“ into your home folder and say yes to the „Replace?“ dialog, you will wipe out your entire ~/config directory, which would be bad. R5 will allegedly include a number of more sophisticated options for handling this scenario.