Constructing a complex system-of-systems (SoS) involves integrating two or more components. When integrations overcome isolating mechanisms inherent to heterogeneous components, a SoS is a software hybrid. SoS designers are challenged to create a viable hybrid that reuses significant value from autonomous, component systems while allowing for new, SoS-wide properties to emerge and be reliably maintained. Thus, a SoS is a super-system integrating many designs, yet not identical to any of them. Formalisms beyond architecture definition languages for mismatch are needed to express SoS designs to terms of the properties and structures that promote the determination of the cause of hybrid failure and its resolution. This paper extends a formal specification language to SoS designs within a paradigm based on software speciation, where software systems experience divergent evolution under various forms of isolation to become incompatible. Examples from security audit are used to illustrate the application of the formalism.