In this second part of our series on the recently proposed many-body expanded full configuration interaction (MBE-FCI) method, we introduce the concept of multideterminantal expansion references. Through theoretical arguments and numerical validations, the use of this class of starting points is shown to result in a focused compression of the MBE decomposition of the FCI energy, thus allowing chemical problems dominated by strong correlation to be addressed by the method. The general applicability and performance enhancements of MBE-FCI are verified for standard stress tests such as the bond dissociations in H2O, N2, C2, and a linear H10 chain. Furthermore, the benefits of employing a multideterminantal expansion reference in accelerating calculations of high accuracy are discussed, with an emphasis on calculations in extended basis sets. As an illustration of this latter quality of the MBE-FCI method, results for H2O and C2 in basis sets ranging from double- to pentuple-ζ quality are presented, demonstrating near-ideal parallel scaling on up to almost 25000 processing units.