Estimating printing time from Cura I know that the actual printing time is longer than the time estimated by Cura, due to acceleration and jerk factor.

However, I have printed a small pyramid for which Cura estimates 4.0 minutes, while the measured printing time is 2 minutes and 40 seconds. 
What reasons could produce this difference?

For clarity, I'm using a Delta Wasp 20 40 equipped with a clay extruder for which parameters such as E-step (for E axis) are unpredictable since I have no filament.
If you properly define your own machine with a delta_wasp.def.json file you can fill in the acceleration and jerk settings of your printer, so that Cura will use the correct values for print time estimation.

For example, take a look at how the Ultimaker 2 is defined.

Exposing these settings to the Custom FDM Printer wizard hasn't been implemented (yet).