I've used that on automated systems. No need to worry about email quota and everything incoming is single-use input for other systems so there's no need to store messages on the mail server
You can do this with IMAP as well, you just need to delete and expunge the emails. Any good email client or library will have an option for this.
POP is literally just downloading all the emails, then deleting them. That's it.
You can't have a script that only downloads emails that match a search (for example emails from a particular sender), since POP doesn't support search. A basic use case is to check for bills/invoices from certain companies and import them into an accounting system, while leaving other emails untouched.
You can't receive emails in real-time and have to instead poll, since POP doesn't support real time notifications. IMAP supports IMAP IDLE.
If you have rules that filter emails into folders, you can't download them via POP, as it doesn't support folders.
For automated systems, if you don't want to store the emails, you can configure the email server to pipe the emails directly to a script. That way they're not stored at all, and your script gets them immediately rather than having to poll.
For submission (connections coming from users that have an account on the server) or for relay/target (connections coming from other email clients)? All email clients support encryption so I think requiring encryption for submission is reasonable. Server-to-server (port 25) can't have it enforced though, like you said.
It's from a era where everyone trusted everyone else. All connections were unencrypted, spam protection and rate limiting weren't needed, and security really wasn't on people's minds. Modern security and spam protection is hacky because it's built on top of protocols that weren't designed for it.
The other major issue with old protocols is that they're stateful. Modern protocols are mostly stateless since it's generally easier to deal with. They've also had more and more features hacked into them over time, so the specs are enormous.
There's been one major attempt at modernizing it: JMAP. It's stateless, uses JSON, and intends to replace both IMAP and SMTP. FastMail started the project. https://jmap.io/why-jmap/
However, they've only looked at the "easier" part to replace: Communication between a user and their email server. They're not looking to replace server-to-server communication at all.