Hi, I have tried your method and the problem seemed to be less evident but, for me, it didn't solved.
So I have tried this: instead of raise the two point where the extruder was higher, I have raised the point where it was nearer the surface and I have started the calibration routine. At the end of the calibration process I have removed the little piece of electric tape and started printing.
In my case this seems to have totally solved: the first layer appeared perfect, no knocking sound during the print and finally I have been able to print (without supports) this: https://www.thingiverse.com/thing:1849355
For me this was the most difficult print because every time near the completion, the extruder was dragging on the surface causing the small base to break.
So I would say (or confirm) that the problem is in the calibration routine and that the fact the extruder is nearer in an area, not only causes the first layer to be not uniform, but also is the cause of dragging on surface (and knocking sound).
All these problems have disappeared for me at this moment and this is the result (sliced with S3D, FS 0.8.3 on osx, Flux red filament v1, buildtak sheet on metal plate) :