Having come to FreeCAD from SolidWorks, ProEngineer, Inventor... other, using PartDesign with it's arrangement of sketches and Pad/Cut/Etc, similarity between those other programs is maintained for sensible design process - if you know one, you basically know the others including FreeCAD/PartDesign.
Sure, you can do it in Part workbench... but, I've taught too many engineers and come away with a standard modus operendi...
Oh, true nothing else was used in PD for this example but, usually I add features to the imported Step and doing it in PD makes it simple for my little brain.
File size comparison:
Freecad Exported cylinder, base and rectangle: 16kb
Freecad Exported Boolean: 16kb
Freecad file with Boolean op and Step files: 14kb
SolidWorks Assy: 137kb
SolidWorks Exported Step (select the 3 parts): 32kb
SolidWorks Exported Assy Step: 52kb