How to properly set up Application Provisioning in ARR?

Question

IIS

Good afternoon!
I have a server farm of 3 nodes, each with IIS. A .NET application is deployed to one of the nodes, after which, using Application Provisioning (ARR), the application is synchronized to other nodes of the farm.
Everything works well, but now there is a need for some application files to be different on different nodes. I could, for example, make changes to the files with a script, after the deployment, but the next synchronization will overwrite these changes.
Maybe someone faced a similar problem? Perhaps there is some way to make exceptions in Application Provisioning for certain files/folders?