Can the Automation API set structured configuration like demonstrated in the docs (https://www.pulumi.com/docs/concepts/config/#structured-configuration)? I've tried

namespace:key[0].property

but not having any luck so far 😕

No, there is an open issue for this: https://github.com/pulumi/pulumi/issues/5506

Ah ha, thanks for that @lemon-agent-27707! I'll keep track of that issue 🙂