First time creation of the actual atlas texture isn't very clear, as you need to know that you have to click the "recreate atlas" button.
The atlaser works so seamlessly that it might confuse a user into thinking it hasn't done anything.
But the primary thing
The texture list is confusing to use when you need the textures in a specific order, visual texture slots in the same pattern as the atlas would make this way easier to understand.
not sure how I would directly solve point 2 tbh, other than a annoyance popup telling you its regenerated, but then it would counter the point of how automated it is....
But the primary thing