Whether you use a custom symbol server or the CLI has no effect on how the file is processed in Sentry. In the end, the Symbolicator service always retrieves and unpacks the file and then runs the same logic on it. This does not happen when you upload the file, but when it symbolicates a crash that requires the file.
The errors you’re receiving ultimately have to do with how we process the file. The fact that you’re able to open the Minidump in VS indicates a potential bug in our PDB file handling. In order to debug this, we would need access to the very file that is causing the issue, however. Would you be able to provide one of the offending PDBs so we can analyze them?
Do you read these errors from logs, or from internal reporting to Sentry? Depending on this, there are different steps on how you identify the file that is causing these errors.