This is the total number of messages on all levels for all the files in the project. Messages in header files are de-duplicated (they are only counted once and not for each source file the header is included into).
This sets the message level from which the message total is calculated. Only messages from this level and above are summed to give the message total which is used for the Messages Threshold comparison. Note that Compliance Index thresholds are not affected by this setting.