How to specify registry entries inside the package created by MakeAppx.exe

We are using MakeAppx.exe (manual packaging) to author MSIX package. Our earlier installer (scripted) used to create registry entries under the hives

HKEY_CLASSES_ROOT (file association, CLSIDs, preview 

HKEY_LOCAL_MACHINE

(The list is attached). 

Please guide how we can configure these with the manual packaging route. Is there any way to author the registry.dat.