That "one-program-one-function" does not mean that you can't have alternatives, especially when there is an alternative view of what the functionality actually is.
Gnus view Emails quite differently from any other mail software. Everybody else think that Emails are something that you don't want to lose unless you press a command to do so. Gnus views Emails to be similar to News and expires in the same way. You are encouraged to configure it to automatically split mails into many groups, each group expires in a different way. Once you get used to it, you'll find that mails and news are really not very different after all, especially for public mailing lists, mailing lists of the company you're working on, and people who will send you mail for exactly one reason (e.g., your insurance agent).
You can say that this is a consequence of putting a round peg into a square hole, but I think otherwise. It gives you a break to have to delete Emails: all you do is to mark it as read (or simply catch up the whole group), the mail will be kept there for a while, and then will disappear by itself when it ages. And you keep mails for mail and news in the same way (using Gnus' "cache" feature), which copy it to a place and still treat it as part of the newsgroup rather than having you to find somewhere to copy to. After using it for I think 3 years, I'm pretty much ruled out from any other mail readers.
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