A web page can have multiple layers, one on top of the other.
From the browser's perspective, a part of a web page is considered visible even if another element is layered on top of it. As a result, sometime, while the browser may consider an element to be visible it might be completely hidden by another element that is displayed on top of it.
Advanced visibility check asks the browser what is the topmost element given coordinates on the window. If the element whose visibility we test is returned by the browser as the topmost element than we conclude it is indeed visible.
This setting is not used by Iridize by default because it is somewhat resource intensive on the browser.
The advanced visibility check can be turned on under the advanced settings of a step or when configuring step conditions.