Causes of over-extrusion?
This is almost surely the source of your problem:


  I had to replace the entire hotend assembly on my Prusa i3 MK2,5. Before that, there was no issue. After the replacement and after noticing the issue, I followed the list above. I recalibrated the extruder and in fact I had to increase the steps/mm to match the extruded length.


There is no plausible physical reason for extruder steps/mm to change due to replacement of the hotend. Steps/mm is purely a function of stepper motor steps per rotation and extruder gear radius. Set it back to its original value.

If the extruded length is not matching what it should, you have a problem with blockage/flow rate in the hotend restricting advance of the filament and causing the extruder gear to grind without moving it, or the motor to skip steps. Adjusting steps/mm to "compensate" will not fix this; it will just grind/skip more. Instead go back to the beginning, with steps/mm set correctly to the original value, and start looking for the cause of your hotend problem.