A mate of mine used to be a civil servant in the Welsh office and he reported the opposite. There was a job (not my mate's) of Assistant Engineer who, naturally enough, reported to the Engineer. The Engineer reported directly to the Secretary of State for Wales. Assistant Engineer was a very very senior position
It's not just the Civil Service - and yes, there were some absolutely bizarre titles when I was there, I'll admit - but I've seen many equally, if not more odd in the private sector as well.