Case one:
First, the total runout tolerance would be apprpriate for a tapered cylindrical application. Circular runout might be a better surface to datum axis A control in that only individual circular elements would be measured relative to the specified datum axis A. Total runout specification would require all surface elements to be measured in a single setup (dial indicator oriented at specified angle to datum axis and then zeroed and part rotated).
If circular runout was applied in this application then the circular runout would control the form and location to 0,1 of each individual circular element relative to datum A. The Profile of Surface tolerance 0,05 is then used as a refinement of form limiting the total surface variations relative to the surface itself. The profile tolerance would be a refinement of the surface form where the circular runout would control the form, orientation and location of EACH individual surface element relative to datum A.
Case 2:
The flatness tolerance is meaningless as the perpendicularity tolerance will control the total surface variations (Flatness) to 0,1. Flatness should only be used as a refinement of form and is always hieratically contained within tolerance boundaries defined by orientation tolerances.