The emissions that occur in one stand in one year, the stand that is burned, are offset by emissions from other stands surrounding that stand that are regrowing. So yes, the stand that burned will take 100 years or whatever to remove the carbon dioxide that was released from the fire, but the forest is characterized by stands of many different ages that are in different stages of their life cycles, and these other forests are removing carbon dioxide from the atmosphere.
What we're doing with our tools is basically calculating the annual balance of emissions and removals of forests that are in different stages of their life, from young forests to middle-age forests to old forests that are all removing carbon. Some of these removals are offset by the emissions associated with fires, insects or harvesting.