What is the point of encryption at rest?
The file_key_management is largely a testing plugin. Its there to show the general operation and be there as self tests. Its also there as a simple reference implementation if you want to write your own.
You are right about every weakness described.
There may be container based applications where the storage of keys used by the file_key_management plugin are only brought together when the MariaDB pod is instigated. With this there may be some risk vectors mitigated.
There are a number of other encryption implementations using the same server API that offer greater protection.