So why is Slic3r way more accurate with it's settings? S3D has the retraction speed and distance settings so it should account for that, plus travel speed and all other layer speeds. If jerk and other firmware settings affect the estimate why can't a form be provided in S3D to enter these values so a more accurate estimate calculation can be performed? I would also suggest an 'Estimate percentage adjustment' in addition to the other values to further fine tune the estimate.
I basically add 30% to get even remotely close to the estimated print time. The only reason time estimates can't be accurate is because of lack of data. The solution is to provide the facility to record the additional setting values required for accurate estimates.