Believe it or not, not even administrator has total control of these keys (without taking ownership). Microsoft started putting policies like this in place as of Windows Vista due to all of the malware they were dealing with.
You would need to take ownership of the entire HKLM hive to get a backup of the entire tree. This is something I do not suggest. They did this permission scheme for a reason.
The export command silently fails on keys it can't read (and continues) whereas the backup command does not and spits out an error because it can't backup keys it doesn't have access to.
I myself would take the route of either taking whatever keys can be exported OR backing up the entire volume as the permission relationships are part of a bigger system than just access to registry keys.
I haven't tried it but you could possibly backup the hive itself (as in the file) without using registry functions if that is what you really want. I bet it will work.