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It mostly seems to be deprecated to encourage developers to use App Sandbox rather than doing custom sandboxing things. With custom sandboxing baking implementation details of system frameworks into the sandbox policy is almost unavoidable, and Apple would really rather you didn't do that as it limits their ability to make changes in the future.

The underlying sandbox subsystem is what App Sandbox uses. Apple can happily rely on implementation details of system frameworks in their policies because they can update them as the system frameworks change.

The sandbox subsystem is what all of Apple's system software uses for sandboxing, as well as many security-conscious third-party programs such as web browsers. It's not going anywhere anytime soon, despite being marked as deprecated.