Yes it is possible, just make sure that during provision you set the correct permissions to the folder.
We also had an application that changed the ini file within the application directory (in this case being a folder in the C:\Program Files Directory) and permissions are retained.
Do keep in mind that if you don't use any profile management tool (UEM or a writable volume or whatever other option you like) this will be done every time you start up the application. The appstack is read only and can't be changed during use. It can only be changed by updating it and adding these specific DLL files during sequencing.
