With e.g. VM or container sandboxing, we can say things like "If there are no vulnerabilities in the hypervisor or hardware, then the agent can only access these files, these network services, etc". Auto mode doesn't even try to provide any guarantees, so it's impossible to reason about. It amounts to just using the models judgment about what's "malicious" or not, a definition which is subjective, changes model to model, and can be influenced by attacker input.
Empirical evaluations of how many vulnerabilities manual vs auto mode let through are not super meaningful because auto mode changes dramatically with model releases, the type of task being performed, whether the attacker is making targeted attacks designed to bypass auto mode, etc. A security feature cannot rely on these sorts of factors if it's to be taken seriously.
Further, percent of malicious tool calls accepted is a bad metric. It's like measuring the security of ssh in terms of what percent of unauthenticated logins succeed. The only acceptable value is zero. It's pass/fail, not a spectrum. So both auto and manual mode should fail equally here. Further, the set of malicious tool calls admitted in auto mode may not be a subset of those admitted in manual mode.