System backups are the bane of Windows. It's why disk images are pretty much the only thing that works.
The problem all goes back to one really bad decision that Microsoft can't easily fix: the Registry. All apps store critical system information in the same 'space' and even modify each other's data. It's not segregated in any meaningful way so figuring which data are owned by which app - which is critical for backing up all data for a specific app - necessary for restoring that single app on a new system, is essentially impossible.
Microsoft tried to remove the Win 7 system image feature to introduce a 'Time Machine' backup system, but it really only stored historical deltas of individual files, not settings in the registry, which meant that if you needed to recover the entire system to a specific date (or even just restore the current system), that wasn't possible.
This new attempt suffers from the exact same problem because Microsoft has become obsessed with form over function in an attempt to be more 'Apple-like'.
PS: There IS a way to fix this: give each app its own "hive". A hive is basically a "layer" in the Registry that gets virtually merged with the system layer. To the app, it looks like there is exactly one app installed: itself. When it writes data to the registry, it's writing to its own hive and sees that layered on top of the real system hive with no other apps' data.
That does cause a problem: currently apps can modify other apps' settings - that would either break or require a new API to request permission to write to another app's hive. But very few apps need this feature and it's a security risk, so it's probably not a bad thing to break.