Here is a stronghold in seed -823932072.  As you can see, the top level of a mineshaft has completely and perfectly overwritten stairway, silverfish spawner, and 'top' and 'bottom' 6 receptacles of the end portal.  

My understanding is that this is generally not something you want to be able to happen and that other constructs have been tweaked to not be able to render end portals unusable (ie MC-173032), and that this is generally something that is regarded as a myth.