I have never done a calculation in which couple-moltype is not specified. Even for mutating a protein in which only one residue changes, that is the [moleculetype] that is being transformed; an explicit B-state is specified for the residue that is transformed and the remainder remains in the A-state.
couple-intramol is integral to the calculation, it specifies whether intramolecular force field terms are coupled as a function of λ. For an absolute free energy calculation, it needs to be set to no but for a transformation like you’re describing, in which the molecular structure changes, it should be set to yes.