You can write scripts to do a lot of the stuff you want.
1. Copy the entire project directory from an existing project to a new directory.
2. Change the names of the .prj and .pcb files.
3. Edit the .pcb file to reference the new project filename
4. Edit the borders.ini file to change the sheet property objects with revisions, if you use them that way in the schematic sheets.
5. If you use Drawing Editor for drawings, you can also edit the files that can be used for all title block properties.
There are a few weaknesses in the Job Management wizard. Since there is no common standard for where in the database file structure you keep your Fablink and Drawing Editor data, there is no way for it to know where these files are and how to change their names. And although it's technically possible to open Fablink and Drawing Editor and go through each placed board/panel object and re-reference them with scripts, it's almost easier for the user to do that manually.
So it's a partial solution, but it's not comprehensive and there is no easy way for it to do everything to make an entire design database ready to go, with all the internal links complete and correct.