MovelessMove-0585 the scenario you are outlining is a bare-metal data extraction operation rather than a functional system repair. The disconnect happens between self-contained executables and structurally integrated software. If you back up C:\Program Files, overwrite the system directory from the WIM file, and paste the binaries back, you only restore the physical data. You dont restore the Component Object Model registrations inside HKCR or the crucial software dependencies mapped inside HKLM\SOFTWARE. Complex applications, deep-system drivers, and the native Windows Installer database dont have the automatic first-setup routines that PC games do. They will crash immediately because the new registry has no record of their required dynamic link libraries or background services.
Using your wimlib extraction method to force a broken machine to boot is a clever way but as a long-term solution, you are left with a fractured operating system. The native Universal Windows Platform apps will fail, the Component Store will throw permanent integrity errors, and you will spend vastly more time manually patching broken application links than you would by utilizing the native DISM servicing stack to properly repair the existing OS.
VP