Yeah I understand. That the files were encoded was what I thought was the issue at first but it appears that its an Apple Mail design flaw.
The Support Engineers just got back to me after looking at a couple of my disk images. It turns out this is intentional for some reason (though not entirely sure about that).
It looks like this is an apple issue. Namely, when I create a fresh mailbox and try and transfer a message to that new apple mail mailbox Apple Mail alerts that the connected email account is offline. (recall this mail was downloaded to the local client as a back up and is no longer connected to the email account that it once was).
So it appears that because the email account isn't actually connected to a "live email". Apple Mail can't attach the attachments to the .mbox file upon export even though, the attachements live on the local machine in Apple Mails own mailbox file architecture as full files.
I'm checking with some colleagues who have older versions of Apple Mail to see if the email accounts they have are connected to an actual webmail or other email account.
If that is the missing link then its on apple mail to fix. If indeed, one has to have a connected live email account, then its by design that Apple Mail prohibits the creation of an .mbox file will full attachments and just creates the messages.
Which seems silly, so maybe I can get them to fix that. It shouldn't matter if an account is live or not, all the email files and attachments live on the local client. It appears that its just a matter of Apple Mail ensuring that regardless of being connected they can export to an .mbox fully with the attachments (encoded or otherwise). The whole thing is really strange. Email is such an old protocol and I am sure Apple wants to focus on numerous other software aspects than silly old Apple Mail though. 😝