How is mbox a broken format? It's a bad idea to use it in a multi-writer environment, and it's horrible because there are competing versions of it. But for plain storage, I thought it worked quite well.
Any line following a blank line and beginning with the four characters "From" marks the start of a new message. The BSD way of handling such lines in the body of a message was to prefix them with ">", which is a non-reversible workaround and is in the uuencode target charset.
Prefixing every line in the message body with a tab character would allow reversing and not interfere with uuencode/base64&c.
I've got mbsync set up to periodically dump my Gmail into a local Maildir archive. Works great, and it was a (relative) breeze to integrate with my old mail archives reaching back to the late 90's.
https://en.wikipedia.org/wiki/Mbox
Sounds like Mail.app exported in mboxcl2, which breaks mail readers expecting the mboxo or the mboxrd formats.
I recommend people to use IMAP for extracting the mail, and to store it in something outside the mbox family.