Code requirement for depth of Counter Flashing and material sealant?
The IRC covers roof assemblies briefly in Section R903 but it's not very specific.

It does say (and this is a common theme throughout the IRC and virtually all building codes):


  Roof assemblies shall be designed and installed in accordance with this code and the approved manufacturer’s installation instructions such that the roof assembly shall serve to protect the building or structure


So if you know what specific product was installed and can find installation instructions from the manufacturer (maybe call them?), then you would have something more specific to point to.

It may also be worth calling your local building inspector and find out whether there are any more specific local building code rules that may be applicable.