Now that ✨ Add an option to disable the add to cart message on a certain order type Fixed was committed, the code in commerce_webform_order that hides the add to cart message can be removed.
That won't be backwards compatible, but that code is now an unnecessary maintenance burden on this module.
Remove code.
Backwards compatability is probably impossible here. We could also add a status report warning if that flag was not set on an order type used in a webform but I'm not sure it's worth it.
Closed: won't fix
3.0
Code
Thank you very much for reporting this, I think keeping this configuration is going to give more options to the user. So I prefer to leave it as it is.