When cars have different internal gear ratios, they will have to run different size gears to achieve the same final drive ratio. Whether this has much of a real world affect between cars has been discussed many times on this and other forums.

In practical terms, there are too many variables to compare between 2 cars whether they are the exact same vehicle or not. Often the reason a particular car is faster is due to setup and/or driver. The best thing to do is use FDR as a baseline when comparing different vehicles. You may need to make some adjustments to gearing or timing of an individual motor to get the best results.

If the original question has to do with one car out accelerating others, it could be any of the following...
Less tire slip due to grippier tires, diff settings.
Better launch due to speed control settings.
Better driver managing speed through the corners (braking/accelerating).