This is because you need to have an onSave on the Form component.
On the Form - use an empty function () => {}, and use applyMetafieldChange on the FunctionSettings onSave prop.
I’m hesitant really to make that recommendation until this issue is solved: Admin UI Extension not re-rendering and not updating data on Discount Navigation
I suppose it’d be useful to understand how applyMetafieldChange actually works. Does it create a change set that’s committed on onSave on the FunctionSettingscomponent?