RE: Dynamics 365 Sharepoint integration. What about permissions?
The way I see it, you have 4 options:
A - You leave things as they are - not recommended because everyone will be able to see everything on the SharePoint side, and I can't think of a situation where that would be acceptable
B - Manually change the permissions on SharePoint - This is better than A, but only for a really, really simple permissions scheme. Ask yourself: what if there are new folders, new users, or new groups of users? What if a user moves to a different group or his permissions change on the Dynamics side? How is someone going to know they need to update SharePoint, and how long is it going to be before they actually do it?
C - Create your own code - This is better than A and B, but it is time-consuming. Again, you need to consider many scenarios and reflect them all in your code.
D - Go for the Connecting Software Solution that you mention CB Dynamics 365 to SharePoint Permissions Replicator, which is, in view the best solution. Besides all the problems you tried to avoid with B and C, you already have a way of solving the unique permissions limit problem (through SharePoint Structure Creator, which is also perfect for organizing all the docs coming from D365.
I hope this helps,
Ana