If I were to log onto a Minecraft server with one of my characters, log off, and then log onto the same server with a different character (which is also paid) on the very same computer, but I'm on a different IP address because I'm at a friends house or using an IP changing program…
Would the server OWNER be able to tell that these two different characters have been played by the very same person?
No they wouldn't be able to tell.
1) As long as the two account names don't look similar, he won't know.
2) He can look up the IP for the account, but if it's 2 different IP's, he's not gonna know it's you.
IP changing programs don't change the IP your ISP assigns you, so you would still appear to be connected from the same IP. Even though you have a different user name, when I see multiple connections from the same IP address I start to get suspicious pretty quickly. There's a good chance that the server owner would indeed be able to tell that it is you.