The thing that really needs to be asked/addressed here is what is being separated, and why. The OP states that:
Every respectable backup guide these days will tell you that the most robust scenario, and one that will minimize the chance you will one day cry, is to keep your data well separated from the system and software.
Now while that is true, one needs to look at the context to really understand what it means. With a server there are performance concerns that require certain type of applications/data to be segregated to prevent fragmentation from bringing the whole shebang to a crawl. Which is why partitions are used to keep log files, databases, & etc. from scattering everything everywhere. So on a server where rapid restores are a must, the partition breaks make things less stressful. But, on a workstation, from a backup perspective, what does multiple partitions really gain you? In reality... nothing. Backup software does just fine following folder trees (and there's no real rush).
Manufacturers trying to out low-ball each other flooded the market with XP machines that had 256MB RAM, a "recovery" partition, and no install media. When the machines started getting a bit old, and XP memory requirements increased a bit, these machines unanimously celebrated by scuttling a hole in the drive right where the pagefile wasn't anymore. Sure, the recovery partition was "safe" on its own partition...but the drive was trashed which rendered it useless also. So keeping your data on a separate partition doesn't really in-and-of-itself solve anything. A separate physical disk, would, but that's not a cure-all either. All of the scuttled-to-death hard drives had one thing in common. They all trashed the pagefile's location, and My Documents was never an issue to recover.
So now you're thinking but viruses could eat my files...Yeah...and hiding them is going to help how? The last really aggressive file eater was Snow white; it ate a very large segment of CBS's archives...which I'm reasonably sure were not in anybodies My Documents folder. Hiding your porn stash might keep mom out of it...but a really aggressive bug, will only take a few milliseconds more before it starts chewing up your stash. In which case software based "real-Time" mirroring, only guarantees that you will have two identical copies of the same damaged file.
Other random "incidents" - Well if you really knew better ... it wouldn't have happened in the first place. But that's kinda the point of backing up (on a regular schedule) to external media. Not to mention that "emergency" reinstalls do not actually require formatting the drive, so even if I do manage to hose the OS I'm still not going to lose anything (parallel installs are quite easy).
Sure nobody's perfect, and anything I have that is extremely critical gets a multi-site backup. Once to my server, and once to the office server. The rest is just backed up to the (local) server.
Do I keep my documents in the default location? No it is on a separate working partition. But that is solely a maintenance issue driven by the high level of fragmentation caused by some of my activities. This allows the contents of the OS partition to remain a bit more static (Circular fixed size logs don't change size).
One thing I thought to add is that mirroring or any other RAID based disk configuration are only availability solutions that prevent the need for downtime and a restore operation if a disk fails, which maximizes uptime. They do not replace or even mitigate the need for a regularly scheduled back to external media.