Warning message on entire site backup fread(): Read of 8192 bytes failed with errno=21

That MR doesn't solve the problem but makes it easier to tell what is going on.
I stole the logic for how to do the file reading from core:
core/modules/jsonapi/src/Controller/TemporaryJsonapiFileFieldUploader.php:356
And threw some exceptions with the $real_path in them.

For me it is an empty folder as well

Could not read the input file: public://library-definitions

For any who land here, I stumbled upon this error trying to create a backup of files.