Can Automator pass multiple lines (e.g. from a shell script) to the New Mail Message action?
It looks like there may be a bug in New Mail Message action in Automator. If you are interested in an AppleScript workaround, where the output of the Run Shell Script action is formed into the content of the new mail message using AppleScript code to create a new mail message, here's an example workaround.

In place of the New Mail Message action use a Run AppleScript action, after the Run Shell Script action, with the following example AppleScript code:

on run {input, parameters}
    set theMessageContent to ""
    repeat with i from 1 to (count of input)
        set theMessageContent to theMessageContent &amp; item i of input &amp; linefeed
    end repeat
    tell application "Mail"
        activate
        set theMessage to make new outgoing message with properties {visible:true, content:theMessageContent}
    end tell
end run


This creates a new message that looks like the following example image.



If you need too, you can add additional properties, as in this example AppleScript code:

on run {input, parameters}
    set theMessageContent to ""
    repeat with i from 1 to (count of input)
        set theMessageContent to theMessageContent &amp; item i of input &amp; linefeed
    end repeat
    tell application "Mail"
        activate
        set theMessage to make new outgoing message with properties {visible:true, subject:"Hello World", content:theMessageContent}
        tell theMessage
            make new to recipient at end of to recipients with properties {name:"John Doe", address:"johndoe@domain.com"}
        end tell
    end tell
end run


Obviously, you'll need to change the value of the additional properties, and or add more properties then shown, to fit your needs. You can look in Mail's AppleScript Dictionary in Script Editor for additional applicable properties.

This creates a new message that looks like the following example image.