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The term "system" can be difficult to define, as it depends upon the perspective of the observer. The classical definition that a system comprises a process with one (or more) inputs and one (or more) outputs is meaningless in the context of SJTAG.
At the simplest level, a system may be any combination of electronic circuit boards which together perform some meaningful function. What is important to realise here is this concept of a system enforces the consideration that a system is a hierarchical entity: A "system" comprising a rock of several PCBs my be a sub-system of a larger entity, and so on, almost ad infinitum.
SJTAG aims to make the Boundary Scan functions of the lowest structural assemblies (typically the PCBs) available for re-use at all the higher levels of integration.