So you have an object in a hierarchy of prefabs like that, which is how things are getting imported by default. And there are million reasons why things should be like that ...
object prefab(empty GO)
object container (empty GO)
mesh1
mesh2
mesh3
mesh4
object container (empty GO)
mesh5
mesh6
and you want to snap your things to another mesh ... but if you select the top empty object container the vertex snap doesn't work for the hierarchy below??? Which means that you can just snap your mesh1 somewhere then your mesh2 somewhere else and then try to bring the empty GOs to fit with your result. Which is simply more work than doing it by hand getting the root and try to match it. Is there any way to snap a whole hierarchy ?