IMO, You probably will never get a definitive answer on this. Even if you did figure out why your printer does this, the next person with this issue might have different results. The reason is that the overall calibration of the machine is affected by so many interconnected variables that it would be very hard to isolate the cause of these minor fluctuations. For example, the combination of your extruder steps/mm, nozzle diameter, and flow multiplier might give good results and changing any one of these could make it worse. However, there probably exists a combination of changing both that will also produce good results. I.E., perhaps you could make up for too few e steps by bumping up the multiplier.
I have a similar issue whenever I swap out nozzles. I have to adjust the multiplier when I change nozzles, or my single wall calibration cube comes out a little small when I go up a nozzle size to 0.60. But I am dealing with changes in the 0.0X mm range, so I usually don't bother. If I had a printer that I never wanted to change the nozzle on then maybe I would.
Anyway, what I'm trying to say is that while slic3r should automatically calculate the changes, there are so many variables that you may always have to make minor manual adjustments when any one is changed if you want near perfect prints. After all, you are dealing with molten plastic pushed thru a hole, there will always be some distortions. I hope that makes sense. Just my opinion.
SD4 w/ RUMBA, E3D Volcano, all bearings, glass bed