Registry importing -- how does it really work?

I was doing some maintenance and part of this involved a full registry backup. I realize that the Restore Point handles this, but just in case I figured it's a good thing to do. Anyway, I got to thinking about what's involved with RESTORING the full registry, something I've actually never done. In the article I linked, it is mentioned how the import adds keys back into the registry. Nothing is said about replacing.

My question is this: Does Windows simply COPY all of the keys it finds OVER the existing keys? Or does it actually do a REPLACE? What I'm getting at here is probably best explained with a scenario. Let's assume we have a registry backup that we're going to import after having run into a registry problem. They are obviously not the same, as changes were made. But, how Windows resolves those changes allows for several possibilities. Let's look at one key for an example:

Current:
HKEY_LOCAL_MACHINE\Software\JoesUtility\Config1\A
HKEY_LOCAL_MACHINE\Software\JoesUtility\Config1\B
HKEY_LOCAL_MACHINE\Software\JoesUtility\Config1\C
HKEY_LOCAL_MACHINE\Software\JoesUtility\Config2\A

Backup:
HKEY_LOCAL_MACHINE\Software\JoesUtility\Config1\A
HKEY_LOCAL_MACHINE\Software\JoesUtility\Config1\B
HKEY_LOCAL_MACHINE\Software\JoesUtility\Config2\A

So, after the backup, Config1\C was created. When restoring the backup registry, would Config1\C be lost, because it's not present in the backup? Or is the import really a COPY, so that anything added will simply be left as-is, but anything fully matching will have the key values updated?

It would really be great if Windows allowed for the option of REPLACE or COPY with the import. One credible reason why to select REPLACE is when you uninstall software that caused problems, but registry entries were left behind. A REPLACE would effectively remove those problem entries, whereas a COPY would simply leave them alone. I realize of course that a registry cleaner could be run to remove any "orphaned" keys left behind, but that isn't guaranteed because some programs may muck around with system level registry entries.