I find that sometimes it looks up the estimates wrong. For example, look at my 1998 GMC pickup. The EPA figures the site pulls up are for the regular cab version, not the larger extended cab that I have.
We have to fuzzy match the vehicles we have to the EPA database, which is why you are given a list of vehicles to choose from. Looking at the 1998 GMC Sierra 1500 5.7L. I only find two available entries, one for manual and one for automatic. I don't see any differentiation based on bed length.
I believe in 2008 the EPA ratings were revised for all previous model years so someone could compare 2008 and newer vehicles with 2007 and older. I think you would only have to redo 2007 and older vehicles.