I had believed with the USA DOT exception the luggage allowance for the
first journey applies for the entire booking.
[EDIT]
However, it appears with the USA Dot exception, the MSC is to be determined by the entire booking - see below.
[/EDIT]
If there's a stopover in BER then there are at least two journies: NCL-BER and BER-LAX (more if this is a return booking). In which case the NCL-BER allowance would apply for the entire booking. (For travel within a IATA Tariff sub-areas, the carrier performing carriage on the first international sector. )
It could be the booking engine used is still referring to IATA resolution 301 - which I doubt - maybe APTCO is not working correctly - anyway that benefits the passenger in this case.