> But what tends to happen, and this is much more serious, is they poison future work and make further modification of the codebase more burdensome and error prone.

Agreed.

Probably better to add whatever instructions it takes so that the agent doesn't write comments, at all, ever. If you need comments to understand the agent's code, the necessary information should already be in a conversation somewhere; and you should summarize it yourself, because the comment will be for your own benefit. Otherwise you are letting past-agent steer future-agent more or less at random.