That is not strictly correct. Windows will allow you to create a system image of your C: drive complete as it is at that time. The option can be found in the lower left corner of the File History setup page and this does not require 3rd party tools to create or use.
The Windows Recovery USB key can then boot your computer in the case of a complete O/S failure and this can detect the image if on an attached drive. It again requires no 3rd party tools.
Upgrading from Windows 8 to 8.1 does not generate a new key, you have a key. What that key will not let you do is install 8.1 direct. Microsoft have relented to some degree and allow you to download refresh media with that key but will still not allow a bare metal install.
In order for that to happen it would require a special setup image that would accept the 8.0 Product ID held within the key even though installing 8.1. Not impossible but a difficult precedent to start. Product ID filtering is a key component of the anti piracy measures being used.
As those specifically with the issue you describe are relatively few it is unlikely to change.