The "Publishing Master Page" content type inherits from the base "Master Page" content type, yet both content types contain the same site columns (see Content Types with associated Fields for SharePoint 2010).
About publishing-enabled content types states "There are six content types that have the Publishing feature enabled." This doesn't really mean anything for the master page though, since the Publishing features are activated at the site and web levels, and the master page doesn't have any effect on this.
The biggest difference here is that it gives you a way to delineate between your standard site master page and your publishing layouts' master page. This is the difference between
SPWeb.MasterUrl (Standard) and
SPWeb.CustomerMasterUrl (Publishing) (see Sharepoint SPWeb - MasterUrl vs CustomMasterUrl).
WROX Professional SharePoint 2010 Development has this to say:
In SharePoint, there are two Master Page content types installed with the Publishing framework. The first is a hidden content type called System Master Page and inherits from the Document content type. This is the Master Page content type that is typically assigned to Master Pages for non-publishing sites and for System Master Pages. The second content type is called Publishing Master Page and inherits from the System Master Page. This content type is typically assigned to Site Master Pages in the Publishing framework.