I accept what you say, but do not see how your company can reduce contingency below that required by ICAO. If your country is signatory to ICAO, then ICAO rules apply. In which country were you flying? Was it a commercial jet operation (which is what I am concerned with here)?
What your described company software does or doesn't do is irrelevant, provided you add the fuel to cover the departure and arrival, which you say is what happens. The software used by the company I worked for certainly covered all these items.
Basically you are correct in saying that you need to get into specifics - that is precisely what I am trying to do here.