R3load based system copy will require downtime of the source system. You basically export the database content to the OS level and export it to the target system. The disadvantages here are 1) downtime of the source system. 2) longer time to do the complete activity.
The advantage of using backup and restore is that there is no need to have the downtime of the source system. You just need to take a full online backup and also the backup of the offline redologs created during that time. Like I have suggested before, taking an online backup do no require system downtime. I don't know what method the DBA used to copy the database. Was he doing the manual copy of the datafiles from the source to the target using OS commands?
Cheers
RB