Hi @Edward Romanenco ,
Yes, this is possible to have two app registrations for one app using multiple authentication schemas or the On-Behalf-Of flow.
There are some examples below:
https://github.com/AzureAD/microsoft-identity-web/wiki/Multiple-Authentication-Schemes
https://stackoverflow.com/questions/55155055/using-two-azure-ad-app-registrations-for-mobile-and-web
Let me know if this is what you are looking for. We don't have an official guide for your exact scenario.
If the information helped you, please Accept the answer. This will help us as well as others in the community who may be researching the same issue. Otherwise let me know if you have further questions.