Extbase repositories are always using storage pid of the current controller.
When you use extbase repository from different extension, the configured storage pid should be taken from the extension this repository comes from, not from the extension using the repo.
I have an extension "my_users" with FeUserRepository and persistance.storagePid set in typoscript
Then I want to use this repository in a controller from other extension called "my_registrations".
my_registrations also have persistance.storagePid set, but to different folder then "my_users" as we want to store registrations in different place than users.
Now, in my controller when you call:
the query will use storagePids configured in my_registrations instead of ones configured in my_users. And resulting in 0 records found.