As far as I know, there are the "Local Values" of project and project suite variables that are stored in those files. That's the primary use of those files as I know it. For the MDS file, there's the path location for any TestedApps that may be configured (since that may change from machine to machine) and the pathing to the log file for the local machine (again, something that may be machine specific).
For the PJS file, it primarily contains the locations of the tcLS files for the projects that are contained within the project suite and, again, the location of the log file for the project suite.
Note that, since these items are machine specific by definition, this is why they are typically not included in a source control system.