Yes it shows up on the print.
In the begining, I believed it was an elephant's foot issue but looking more closely I noticed it was not the first but the second layer that was impacted. Slicing with Prusa (or Slic3r) does not give the problem (and worse, reloading their generated gcode in Cura shows a perfect second layers)
This said, I checked with Notepad my gcode and you are right: all external perimeters are perfectly aligned, the cause is not an expanded second layer. In fact, when I move the sliding cursor down to show the 3 first layers only...
Doing so, I can clearly see that it's the width of the second line that seems the real issue, not its xy coordinates ! It looks like there is too much extrusion. I will investigate in that direction.
When I switch on the "relative extrusion" and I reload the generated gcode, Cura does not display the line width anymore (strange but coherent with an extrusion issue), they are all thin blue lines. I will test a real print in relative extrusion to see if this might solve the problem.