Regarding the E-step in Cura
I can only weigh in on the Marlin side of your question - "The value 500 is intended as mm/min" - uh, no, AFAIK it's steps per mm, just like it says - i.e. with filament, 500 steps per mm of filament fed. Other than not allowing the feedrate parameter to go so high that steps are skipped (which is a different limit) it's time-independent. I suppose with an extruder it would be mm of piston movement, but I don't have an extruder.

In my case, an actual value is closer to 250, and I typically check the calibration with 50 or 100 mm of filament feed so I can make a decent measurement.

I also wonder if your firmware knows it's running on a delta, since mine reports "A, B, C" rather than XYZ and all three towers are the same steps/mm - the "default values" you are looking at might apply to a typical cartesian printer where the Z axis is threaded while the X &amp; Y are toothed belts. 

Assuming it runs correctly you might be seeing irrelevant "default values" and having correct values loaded from EEPROM when the system starts (look at the log window when the control system connects to the printer.)