By flat file I guess you are talking about jbod as opposed to stripping to one large drive letter composed of multiple had drives. I think the consideration is the cost and hassle of redundancy. In my experience hard drives that work when they are first put in service tend to keep working. I have replaced older smaller hard drives with newer larger hard drives in the computer and then restored data to newer drive from direct attached storage. The backup program in Windows 7 works fine for this and I have not tried alternative backup programs and therefore cannot compare alternatives.
However, Windows 7 wants to do a complete new backup every couple of months. So you either need enough space for two backups or you have to delete the old backup for space for a new backup. It takes about 30 hours for me to backup 7TB. So, I have time and the cost of space considerations vs. the likelihood of of a catastrophe of a simultaneous hard drive failure in both the computer and the storage unit. If the catastrophe happened I would lose data, but then I am not backing up accounts due which would put me out of business. The cost of no risk of losing data is high.
Anál nathrach, orth’ bháis’s bethad, do chél dénmha