I am not aware of any differences between a "show run" and copy config but I honestly haven't tried to copy the config off using show run and then load it back onto a switch.
One thing to keep in mind, by default passwords are not stored in the config file. So if you copy the config off, factory reset the switch and copy it back on, you won't have any of the passwords. You can use the "include-credentials" command to store the passwords int he config file in a hashed way.