In v36.0.21+, v37.0.14+, v38.1.8+, and v39 and later, by default, the system processes both EML files and their attachments. The system creates a PDF from the content of the email's body, and processes each of the file's attachments as a separate document in the submission.
If you do not want to process EML files' attachments, add the following to your ".env" file:
PARSE_EML_FILE_ATTACHMENTS=false
When PARSE_EML_FILE_ATTACHMENTS is set to false, the system ignores the files attached to ingested EML files.