They aren’t really “extra”. Every distro uses a different subvolume layout.
@cache is created because there is no reason to take snapshots of your cache. It is totally disposable data so creating that subvolume removes it from the snapshots of @.
@log is created for the opposite reason. By keeping your logs outside of @, if something goes wrong and you need to restore a snapshot of @, your logs won’t be overwritten so you can still access them and see what went wrong.
var/lib/portables and var/lib/machines aren’t created by the distro, they are created by systemd. It should be safe to just ignore those.
That being said, if you want only @ and @home you can remove @cache and @log Alternatively, if you would prefer to re-install, the subvols that the installer creates are in /etc/calamares/modules/mount.conf and you can edit that file before running the installer.