Can a UK ship have different sections of its crew employed under different contractual terms, e. g. some on a BSF agreement and others on NFD agreements?

Yes. 

In some cruise ships, for example, the officers are on a BSF Agreement with employer “A” (with an address in the UK), while the deck and engine room ratings are on an NFD Agreement with employer “B” (a Cyprus ship management company), and the hotel staff are on another NFD Agreement with employer “C” (a Hong Kong hotel staff agency). Each agreement is on a separate form ALC 1(d) (see below) bearing the relevant employer’s name and address, but all agreements must be contained in the same ALC 1 outer cover.