As mentioned in the comments, extrusion stopped working altogether at some point halfway through a Benchy print. Once I had opened compressing lever of BMG clone extruder, I observed that gears were loose, after disassembling the extruder noticed that both extruder side and stepper motor side gears were also loosened at hex head screw keys which were keeping them in place. I ordered a thread locker to address that at another time, seems like vibrations due to constant retractions loosened them.
After tightening and reassembling, issue is not bad to the point prints would fail to start, however filament is not primed enough, so some of the skirt print will be blank.
I also added this with 608Z bearings for supporting the smooth movement of spool. Turns out 608 bearings are widely available almost everywhere, roller skates and skateboards use them, so there is a good chance your local sports shop will have it, too.
I installed Octoprint on my laptop to work around this issue as below:
G92 E0 ; Set Extruder position to 0
G1 E100 F200 ; Extrude 100 mm slowly. This is to make sure hotend is not empty and material flow is consistent, i.e. adjust temperature if necessary.
Only then I start my prints.
I learnt that using E<integer>
to extrude and E-<integer>
retract, I can replace filament too, by using big enough numbers like 350 mm, so I don't have to fiddle with compression lever or its adjustments anymore.
Update: I found more mechanical problems. This issue is not software related. Please see useful advice in comments regarding retraction/priming as an improvement if not solution to this problem.