Extruder calibration --> via extruder steps or extrusion multiplier in Slic3r?  

Extruder calibration --> via extruder steps or extrusion multiplier in Slic3r?

Dear community,
I noticed some over-extrusion aka roughness of the top layer on my prints (have been only printing Prusa PLA or colorFabb PLA/PHA so far) ...
When I check my extruder calibration following these procedures on All3DP ( https://all3dp.com/2/extruder-calibration-6-easy-steps-2 ) or on Matt's Hub ( https://mattshub.com/2017/04/19/extruder-calibration ) I see a slight under-extrusion with the "stock" value of 280.0 steps ... approx. 5%. For clarification, I was just checking - not changing the value yet.

This is what Prusa says on the extrusion multiplier - https://help.prusa3d.com/article/d9j1xdg7vj-extrusion-multiplier-calibration - the pictures are interesting to compare ...

Now, when I print a 20mm calibration cube with the standard Prusa settings for PLA (extrusion multiplier is at 1.00 & "M221 S{if layer_height==0.05}100{else}95{endif} is active, not commented out) there is a slight over-extrusion visible at the top layer (some excess material at the corners) which goes away when I reduce the extrusion multiplier to 0.96 or more.

Standard Slic3r settings for Prusa PLA

Here the extrusion multiplier setting is extreme, at -10% ... are there microscopic gaps?

Is my understanding correct that in the way Slic3r is programmed it transforms an under-extrusion on hardware-side into an over-extrusion on the finished product? This would mean that I don't have to play with the extruder steps but just with the Slic3r settings, and probably per filament type ...

Cheers,
Mark