because encryption in transit != encryption at rest.
Maybe you don't trust the server you are scp'ing the data to, with encryption at rest you dont' need to.
That's not what the documentation is about, though:
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Use GPG with the cipher AES256, without the --armour option, and with compression to encrypt your files during inter-host transfers.
GPG
Encryption helps protect your files during inter-host file transfers (for example, when using the scp, bbftp, or ftp commands). We recommend GPG (Gnu Privacy Guard), an Open Source OpenPGP-compatible encryption system.
If your goal is to transfer securely from person to person, 'scp' generally means there's a common server you're accessing - not that you're 'scp'ing directly to the other user's machine. Keeping it secure when "at rest" on the remote server would ensure it's securely transferred between the two end points.
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Use GPG with the cipher AES256, without the --armour option, and with compression to encrypt your files during inter-host transfers. GPG
Encryption helps protect your files during inter-host file transfers (for example, when using the scp, bbftp, or ftp commands). We recommend GPG (Gnu Privacy Guard), an Open Source OpenPGP-compatible encryption system.
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scp shouldn't be in that list.