How are stratigraphic limits defined before the Phanerozoic?
The standard stratigraphic nomenclature is a chronostratigraphic system based on palaeontological intervals of time defined by recognised fossil assemblages.


That's wikipedia for you. This is incorrect. The point of a Global Boundary Stratotype Section and Point (GSSP) is to identify a global boundary with a very specific archetypical example. While a recognizable and global fossil assemblage is preferred, sometimes there are better choices and sometimes such assemblages don't exist.

For example, the stratigraphic boundary that marks the start of the Cenozoic Era, (and the Paleogene System, Paleocene Series and Danian Stage) is a millimeter thick layer of fossil-free clay near El Kef, Tunisia. This clay layer was laid down about 66 million years ago and can be found in many places around the world. This layer is distinct, unique, and occurs worldwide. That clay layer contains the remnants of the dinosaur killer asteroid.


  How are stratigraphic limits defined before the Phanerozoic?


Getting to point of the question, the base of the Ediacaran "is defined as the base of the Marinoan cap carbonate (Nuccaleena Formation) in the Enorama Creek Section of the central Flinders Ranges, Adelaide Rift Complex, South Australia." The GSSP is the archetype, but as with that thin layer of red clay, this layer of cap carbonate can be found in many places around the world. That layer of cap carbonate represents when a worldwide glaciation event ended.

All of the International Commission on Stratigraphy boundaries that predate the base of the Ediacaran are currently defined in terms of time called Global Standard Stratigraphic Ages (GSSAs). That's a fancy name for a rather arbitrary point in time.