In 1.20.1 forge 47.2.0 there does not seem to be any config options.
I have the config in waystone for only allowing creative players to interact with Waystones that are generated but Towers of the wild does not seem to be effect by that.

I do not have configs created for the mod unfortunately, and do not know how I would create any.

But can you read the waystone config and make yours generated correctly please?

Is this issue still on-going? I was not encountering this issue in my testing