"Altitude" always refers to above see level.
What happens if Ground level is 3000AMSL?
In that case, it would be impossible to use this exemption.
(This is quite sensible, actually, once you realise the main use of the exemption. In the UK, all night flight outside controlled airspace must be IFR. If you don't hold an instrument qualification, then you must maintain 3km viz and clear of cloud, so effectively you're flying visually, but you must still follow the Instrument Flight Rules.
Over most of the UK, the terrain is low enough that most visual flight will be below 3000'. Therefore, if flying visually at night, you will be exempt from this particular rule. About the only places where the terrain is high enough to force you to fly above 3000' are mountainous areas. And if you're flying in mountainous areas at night, then you probably ought to be flying 1000' above the highest obstacle within 5 miles - basically that means flying at or above your MSA - anyway.)
FFF
-----------