Hi,
Indeed. In "list" mode, each add to cart button has its own form. And the options are outside of these forms so they cannot be taken into account during the add to cart.
If you need options / custom item fields, you need to use another display mode for your characteristics.
Regarding the notification box, I'm not sure why it's doing that.
The HTML of the notification box is added there, above the button, similarly to how it's done when there are no variants on the product.
I would need to study the differences between both to see what's causing this. It's probably some custom CSS affecting one and not the other. However, the popup disappears after a few seconds so I'm not able to look at the situation for long enough.
I would need you to change the delay in the settings of the cart notification plugin so that the popup displays for a long time.