We have restricted the allowed attachments to .docx, .pdf, .jpg, .jpeg, .png, .xlsx, .txt, .csv but a user was able to reply via email and attach a .msg/.eml file.
My testing gives the same result: unable to attach an eml or msg through the portal at ticket creation or a response but can include an eml or msg via an email reply. The msg file is converted to an eml somewhere in the process, the ticket shows the email reply with eml files.
