@cadet, thank you for sending this feedback!
I agree that the e-mail would be more useful if it didn't lead to confusion about any of the points you mentioned.
To answer your questions (which hopefully will be clearer in a future revision of this e-mail):
There could be more than one for one site?
Yes, that is possible. One example would be if you have a content delivery network (CDN) that serves your site to the public, as well as your own "origin" server containing the authoritative content for your site. In that setup, both of them might have certificates covering your domain name, but the certificates would be issued to, and used by, different servers run by different people. The CDN version might also have additional names on it, for other people's sites or for other sites of yours that are also hosted by the same CDN. So the names on the two certificates might overlap without being identical.
Another example would be if versions or variants of the same site are provided inside and outside of a corporate network (one version for employees and one version for the general public). Even if the content on the two is the same, it is possible that they would be accessed in technically different ways which might lead to, as in the CDN case, having two different certificates that are present for the same name on two different servers or server configurations.
Why? does it take a long time to renew?
In this case, the idea is to leave a considerable safety margin in case the renewal fails for some reason, like a server outage or misconfiguration. This is especially important when people are renewing their certificates manually, or when people are unfamiliar with debugging a renewal failure, because it's always sad when people show up on this forum saying "my certificate expired yesterday, my site is down!" or "my certificate will expire tomorrow, and I don't know how to renew it!".
The safety margin of one month means that people will typically have one month to figure out these problems before they actually lead to an expiration and unavailability of the site. That is much less stressful for everyone involved than it would be to leave it to just a couple of days beforehand, especially if the debugging process is going to be complicated or involve a user having to research something or coordinate with other people.
When the renew process is fully automated (as Let's Encrypt strongly recommends), renewal usually completes in less than a minute, assuming everything is configured properly. But threads on this forum about getting to the bottom of renewal problems often take 2-4 days of discussion, especially if the person asking the question is in a different time zone from people trying to help.
I am surprised that Let's Encrypt can't tell that I have a valid up-to-date cert for the website that is far from expiration. Why else would such an email be sent?
The likeliest case is something like the public service vs. private service. Many Let's Encrypt certificates are only ever used on internal networks that aren't directly accessible to the general public. So Let's Encrypt can't tell if those certificates are in use or not, but can tell whether it remembers having issued an updated version or not.
This has caused confusion on a regular basis for many years, though, because Let's Encrypt is trying to be very cautious in case users have setups where they intentionally have multiple overlapping certificates at a time. As I discussed above, this is totally possible, but it's not the most common case, which in turn means that most renewal warning e-mails in this situation are false alarms. It doesn't seem that there's any way that Let's Encrypt could determine that automatically, since in the non-publicized-origin-server situation or the internal-corporate-service situation, the place that the certificate is actively getting used can't be located or tested by an outside partly.
The sentence about "If you've replaced this certificate with a newer one that covers more or fewer names than the list above" is supposed to reassure people in this case, but it's fairly common that people either don't read it or don't realize that it applies to their situations.