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An interesting question, and something I never really thought about because I host my own mail server which has daily backups.
Do you actually have an option to export folders from Thunderbird? I couldn't find anything so maybe you're using a plugin to perform that function?
As for format, I think the .eml files are more universally recognized if you want to transfer your message to another client. I have avoided mbox for years because it packs everything into a single large file -- handy if you want to copy it somewhere else, but a pain to work with if you're trying to find a specific message and the more emails you have stored, the slower it gets. Another option which you didn't mention, but maybe you have available (this is what I use on my mail server), is the maildir format. This stores every email as individual files in their named folders, and in plaintext format so you can open them up in a text editor or search through the files with command line tools. Since there is no compression it takes up a lot of space but I find it worth the storage.
If you have mbox or maildir file backups, one option would be to spin up a local mailserver of your own that acts as a relay to your email provider (or even multiple providers or mailboxes). This option might also work to download a copy of all your folders without having to do a full backup from your client, but that probably depends on how the server is configured. The point, however, is that if you have a local mail server running with a full copy of all your emails, then you would now have the option to simply back up the server files as a whole. You can even do recursive backups from a daily script so the task is completely automated and then you don't have to remember to perform the task on a regular basis.
Anyway, just some things to think about.