I am not entirely convinced if we should split the tag. I feel they are inherently the same thing - Webapps in the desktop. Whether they are created through the Google Chrome or Firefox's Market Place or Epiphany web apps, they are very much the same thing.
But, on the other hand, I also feel that having a tag serving multiple purposes is not really a good thing. I feel that we should try to disambiguate the webapps before it gets out of control.
Right now, the majority of the tagged questions are talking about the Unity webapps and I think we should instead tag them as unity-webapps to better differentiate these questions from those that deal with the traditional webapps concept.