1) It seems to be possible to add factors to supply units. Why would you want to do this? What purpose do these factors serve if they are in the supply unit?
2) What is the difference between cities with their names in "Red" and those with their names in "Black"?
1-- An enemy corps can enter a region with a completely undefended depot, remove it (possibly breaking your supply chain), and keep going. It'd have to stop and win a battle to remove a defended depot.
2-- Cities with red names are capitals of the district or province.