To compare the print results of Cura and S3D is not fair!
Cura is a 1/2 or even a 3/4 automatical program that will print very well, when all parameter of the printer and the filament-material are in a certain range of standards.
S3D does it not so, S3D musst be turned from the first point to the last point. There are only basics but that is not sufficient. Therefore you can feel free to use even really exotical materials.
Your ExtrusionWidth is only 0.40 mm while the nozzle is also 0.40 mm. That is ok when you adjust the perimeters to a thin wall so as you do it when you only use it with 2 perimeters. BUT your LayerHigh is 0.2 mm, will say it is 50% of the extrusion width.
If 0.4 mm is not needed, print the ExtrusionWidth with the standard from S3D, that automatically 120% of the nozzle-value = 0.48 mm
LayerHigh is 0.20 as written above 50% of the ExtrusionWidth. The nozzle presses the material very hard and therefore the sidewalls of the extrusion become more and more round and bulge outside.
May be ok, BUT ...
you are printing very, very slow -see below-
the setting of 60 mm/s seems ok but there are also 50% for Outline-Underspeed. When only printing 2 perimeters, 50% of material is printed with a speed of only 30 mm/s AND additionally you have set Speed Overrides below 15 sec one layer down to 20% (of normal speed of 60). Because your model is very smal the printer is therefore running only with 12 mm/s all the time.
What makes that?
The tower has 20 x 20 mm and is the only one object to print. That cause that the hotend of the printer is moving only in this area all the time while the coolling - even with 100% - has no success because there is no place for the fan wind so that the top of the print has no efficient cooling. The hotend heats with its heat-emission the upper layers additionally what is staying smooth.
I could study how the extrusion has pressed the second layer out of the walls vertical line and that are your lines in the surface.
The same lines are inside the tower.
If you want to test something, don't use a such small object. a cube or a tower must be minimum 50 x 50 mm and the best results you can get needs a second object 10 cm beside the first one to win time for cooling. Without harden the upper layer you will have anytime such lines caused be the pressure of the nozzle.
There is another curiosity of your settings.
Scipts - Starting script - has M - commands, M 201 and M205. That concerns the acceleration and the jerk and set them very deep. Using your proflie my printer was very, very slow and also very noicy and has written these values to the eeprom. Unluckily I dont remember the true values of mine but I set them now to M201 > X1000 Y1000 and M205 to X20 *), may be to much but is running.
I dont know your printer and its firmware but the M205 commands parameter are X4 Y4 . This Y-parameter seems to be not existing. Have a look to this link:
http://reprap.org/wiki/Gcode#M201:_Set_ ... celeration
*) M205 X20 is NOT the X-axis, its a parameter for both, X and Y axis!