Well,
mergemaster(8) is only used to merge base system configuration files during upgrades, and
/etc is the only directory where
mergemaster actually does anything.
If you're using the same release on both systems, and actually intend for them to have identical configurations, then just copy everything over. You might use
tar(1) to keep things simple.
If you intended to use only a few options from each configuration file, you'll have to edit them by hand. Even if
mergemaster could merge files between machines it wouldn't really make the process any faster or easier, since it will first look for every instance where configuration files differ; then show you a complete diff of the files; then ask whether you want to keep the current version, replace it with the new version, or merge the files; then go through the differences line-by-line if you choose to merge them.
EDIT: Now that I think about it, there is a way you could use
mergemaster between systems, though it might not be worth the bother. You could mount the root directory of the target system somewhere on the origin system, either directly or using NFS. You could then run
mergemaster with the
-D /path/to/target flag. It would be the same process you would use to upgrade a jail, only you'd be doing it to a bare-metal system.
