Because SPIR-V can be consumed by multiple client APIs, which have different requirements, there needs to be a way to distinguish what is valid for each API. The capabilities system is used to establish what is "features" are valid.
Example: Something such as Builtin::PrimitiveId will not be found in a compute API such as OpenCL, therefore the capabilities prevent an OpenCL targeted SPIR-V module from being valid if the
PrimitiveIdbuiltin is used.
It is up to the client API to properly expose any capabilities that are supported (Vulkan example).