Understand the container
EML commonly represents an internet message with headers and a body, including MIME-encoded content where present. MSG is Microsoft's structured format for an individual Outlook item, which can include message properties, recipients and attachments. An MSG extension is not restricted to ordinary email messages. The available fields depend on the source and how the file was produced.
Compare like with like
A message saved as EML and the same displayed message saved as MSG will not have the same file hash. That is expected for different byte representations. Compare relevant content and properties as well as the whole-file values, and preserve the original export containers. Record whether text was decoded, attachments were extracted or dates were normalised.
Native does not mean unquestionable
A supplied native-format file may have been edited, generated or selectively exported. Assessment must consider provenance and corroboration. Ask for the original account or store context where available, along with details of the export tool and settings. Report fields that are absent rather than filling them with guesses. The useful output is a documented account of what the supplied representation contains and how it relates to other evidence.
Sources & further reading
Primary references support the technical explanation. They do not establish D3 validation of a particular method.