We only have a simple average of applications and the result would be a simple average on the system level. The results that you see on the HD Dashboard's homepage is the system level result. For the results based on size - LoC and Total Quality Index, the tile "Application Map" is to be opened so that it can show the results for different applications.
The larger the size of an application tile, more the LoC and smaller the tile of an application, lesser amount of LoC. And for TQI, if the tile of an application is Red in colour then it has less TQI. And the tiles of application which are green, have higher TQI.
Yes, HD tags and categories are stored in the CSS schema.
If two different deployed HD's are pointed to the same Measurement Base, then the HD Tagging stored for one dashboard will also come on the other dashboard.