ssh-keygen -l -f /etc/ssh/ssh_host_rsa_key.pub
ssh-keygen -l -f /etc/ssh/ssh_host_key.pub
ssh-keygen -l -f /etc/ssh/ssh_host_dsa_key.pub
I get three different fingerprints one for each.
And any of the three is good enough. Which one is used depends on host key algorithm agreed on by client and server. IFAIK ssh_host_key.pub is used for SSH1 and the other two for SSH2.
When I use WInSCP to login with a regular username using a virtual domain on the server, a domain different from the server's main address, I get the RSA key fingerprint, not the fingerprint for the Authorized_keys file, so I am assuming that this is OK, is it?
I have explained this already:
File 'authorized_keys' contains public keys of the user, not the server's. Public key of the server is global for all users, not specific for each one.
In other words, in 'authorized_keys' you give public key to the server, so the server knows it in advance before you connect the first time with your private key. It is the same procedure as when you get in advance the public part of the host key. Just in an opposite way.