When you enable server-based SharePoint integration, you are asked to enter the URL of one SharePoint site where you want the documents to be stored in folders that correspond to records in an entity. But you are able to select multiple entities.
But SharePoint promotes flat IA. We have a Loans site with hundreds of folders, each for a loan deal. And we have a CDS Loan entity - that seems simple enough - for every loan record in CDS, a corresponding folder exists in SharePoint. But we also have a site for "Programs"; each program has its own program documentation, curricula, budgets, etc. And there is a CDS Program entity. Conceptually, loans belong to one or more programs and one account belongs to one or more loan. So Account and Loan are 1:n but Loan and Program are n:n, meaning on the SharePoint side you can't nest loan folders inside of account folders inside of program folders.
As it is, staff go to the Loans SharePoint site to access their loan deal folders - it looks clean and can be filtered by metadata on the folders. Staff go to the Programs SharePoint site to access the folders for each program - looks clean, can be filtered by metadata. These two types of folder cannot be in the same site because the folder metadata is different.
How should this be handled in d365/model-driven power apps? You can't just have one site in SharePoint.