They’re not using a different protocol for delivery, they still use IMAP and SMTP, but other mail clients can’t decrypt the message content from Proton because they don’t have the keys (and nor do Proton). Proton do supply a “bridge” app if you want to use your Proton mail with a desktop email client, which handles the decryption between your computer and Proton by accessing the Proton encryption keys on your computer.

TLS is like a padlock on a box, and you have the key. Encrypted content is if the letter in the box is also written in code, needing another key to translate into plain language.