IMHO, the best solution is to use the value specified in the mission file as the orbiter dry mass. Otherwise, simulating something like STS-93 will require a lot of extra mission file entries, and a proper simulation of all the systems affected. If we just have a single "TotalDryMass" entry, we can specify that the RMS and EDO pallet (when we simulate it) are not installed, set the removed tanks to be empty, and put the correct dry mass in the mission file. This seems simpler (both for programming and creating scenario/mission files) than specifying each component that has been removed.