Apple Mail issue on Big Sur is a REPEATABLE ERROR.

Yes, POP is old, and Apple has been pushing people away from using POP for several years.

Even to create a POP account requires a non-obvious trick: when you add a new mail account, POP is nowhere to be seen.

You have to simulate creating an IMAP account, put in a wrong password and only then you see an option to choose POP.

That said, I still two POP accounts, that were created many years ago, and they still work in Big Sur.

Regarding deleting from Server: the option is still there, see the image below. I have it "after one week", because I want the opportunity to also download some of these messages on my iPhone and iPad. But it can be set to delete immediately when retrieving, as well.

There have been numerous reports of POP3 bugs in Apple Mail since Big Sur. Make sure you file bug reports to Apple via the Apple Feedback Assistant: https://feedbackassistant.apple.com, posting here isn't going to help much at all. The Feedback Assistant gets your bug reports to the actual macOS developers who are the right people to fix a POP3 bug.

The Post Office Protocol version 3 (POP3) was last changed in 1996, 25 years ago!. It is highly recommended to migrate from POP3 to the far superior IMAP4 which is designed for multiple computers to sync email. Most ISP's are defaulting to IMAP4 lately and POP3 is extremely old and limited.

IMAP4 was designed to sync mailboxes between multiple computers. Delete an email and it's removed from the mailbox and subsequently all the other clients see the same thing. Mark an email read and all the other devices will see the email is marked read.

POP3 is meant to have the mailbox emptied when downloading email. There have been options to keep email on the POP3 mailbox for a period of time to help facilitate sync but it's an ugly workaround compared to IMAP4. It also does not sync the read / unread status across computers nor flagging nor tagging of emails, etc.

The alternative it use another email client for your POP3 mailboxes.

Depending on if that UNIX Server with the 15 POP accounts was setup properly. You might just need to obtain the IMAP4 connection information and see if you can login to one of the 15 mailboxes using IMAP. If it was setup properly, all your email should just appear via IMAP. If it wasn't setup properly, well then you are going to need some expert help to configure the UNIX Server. Most mainstream ISP's would offer POP / IMAP / Webmail and they would be encouraging people to use IMAP over POP.