To put this into perspective :
The Captain is the legal authority for the ultimate safe conduct of the flight. Any deficiencies would ultimately fall onto their shoulders. When they sign the various legal documents, such as the tech log, and the loadsheet, they do so acknowledging that they are satisfied the aircraft is fit to fly in respect of its technical state and loading at that point in time. That technical state and loading may well have devolved to other individuals and agencies, but the certification requires that the Captain (and they alone) must satisfy themselves that whoever has been involved, they are satisfied the aircraft can safely and properly dispatch in that condition.
In the execution of this process, the Captain (Commander) will have been provided with a whole raft of input : Flight planning computations; Weather forecasts; Notam information; Crew hour limitations; Aircraft servicibility reports; Load projections and content; ATC delays. On top of this they will have discussed most of these aspects with the First Officer, engineers, Senior Cabin crew, dispatchers, etc, as and where it is relevant and applicable.
As far as fuel dispatch is concerned. The information will have either been calculated by a computer programme, based on a set of variable inputs. From a dispatcher based on similar information and further real time information. Or manually from tables, and human computation. Whatever the method employed, the Captain has the authority, and indeed it is part of his legal mandate, to ensure that whatever adjustments that he considers necessary are applied. This may be a result of his experience, knowledge or simple gut feeling. If the company wish to question his decision, it is their right to do so, and normally they should be satisfied with the explanation given. If anybody else wishes to question the decision, they would be right do so in preventing an error or pointing out a possible error or deficiency. Provided such an error was not the issue, then the Captains decision would be final.