Apart from the user accidentally (permanently) deleting the email confirmation message or glitches with POP3 client email handling, what other scenarios or instances merit the use/need for a "Resend confirmation e-mail" link?
The link doesn't have to be a last resort to be useful to the user.
You've noted a couple of situations where the message is permanently lost, and the user has no other recourse but to find the resend link. Obviously the link is technically necessary for those situations.
But imagine this: a user eager to get started has waited a minute, not seen the confirmation, and started to suspect their spam filter. They click the button disabling their spam filter, and immediately want to resend the confirmation. It's not literally a last resort -- they could go scraping through their spam folder.
Similarly, a user might want to use the tool on their work computer, but be signing up on their personal phone. They realise a moment too late that they forgot to switch on an email forward to their work email. They could re-type URL, or just activate their forwarding and click the "resend" button.
These are examples of users wanting to "do that again", when they may technically not need to.
Also, I can imagine the metrics of how many people click that link might give the site owners an interesting insight into their email confirmation system.