According to https://www.microsoft.com/en-us/download/details.aspx?id=35474 to integrate with Office as a cloud provider you need to add a registry entry under HKEY_CURRENT_USER\Software\Microsoft\Of...
Have you tried creating a modification package that contains this registry entry?
The files and registry contained by your modification package will be merged at run-time with the ones from the original MSIX package you have for office, so you should get the behaviors described in your request.
You can create it with the MSIX Packaging Tool or with other tools like Advanced Installer.
Disclaimer: I work on the team building Advanced Installer.