Hi,
Ah yes, that option has been moved.
But it's still the same, if you deactivate the fields there they won't display in the registration form of the checkout.
The registration form of the checkout will create a Joomla user account, as will the registration form of Joomla, so it's normal that the fields enabling/displaying on the registration will change the display of the fields on both registration form.
That's the way AcyMailing developed their custom fields.
If you want fields to display on one registration form and not another, I don't see any way to do that with the options available and it will then require that you modify the code of AcyMailing. I would recommend that you contact the AcyMailing support in that case. Maybe they know something I don't and they should be able to give you the necessary modifications if that's what you want to do.