It was suggested to me that I should not only save my EX-1 files by bringing them to my drive via XDCAM Transfer, but I should also use Clip Browser and save all of those files as well. I'm editing in FCP. Is this overkill?
Not at all. Think of the actual BPAV folder on the card being the EX version of a tape. It's got everything you need to create new video clips for both Windows and Mac platforms if you need to re-edit or give the raw files to someone else in the future. Most of us are archiving the BPAV folders somehow, either on data DVD, Blu-ray, XDCAM Disc or a simple USB hard drive.
Think of the MOV files from Sony's Transfer Tool as your own particular version of the raw clips converted just for editing in Final Cut Pro.