It’s mostly about the “fan out”.
When you send an email to 50 recipients via Librem.One (or any other email server), you send one copy to Librem.One, and Librem.One takes responsibility for identifying how many unique domains there are among the recipients and sending the up to 50 copies.
When you send the email yourself one at a time, you generate 50 times as much network traffic for yourself (and it takes 50 times longer, all other things being equal). If you have a fast internet connection, maybe you wouldn’t care.
But you are right, a spammer can spam victims one at a time. That has the advantage that the email content can be personalised (via mail merge), which makes it more likely to get through (not blocked as spam on the receiving side) and more likely to influence the recipient.
So if the spammer is spamming victims one at a time and using someone else’s mail server to do it (in this case Librem.One) then a diligent mail server has to apply recipient rate limits across multiple emails and not only apply a recipient limit independently to each email sent e.g. a limit of 50 recipients per hour whether sent as one email to 50 recipients or 50 emails each to one recipient.