Is it possible to merge two collections with the same name?

At the moment if I merge two parts of a graph it only takes the objects in a collection from the last input.

The Merge LOP won't handle this case; it is essentially layering each input's layer stack together, with the last input strongest. You either need to generate your collection afterward, or make each input have a unique collection, then make a new collection out of those 3. USD does support a collection made out of other collections.