Modelcheck help indicates that you can combine several start files into a single configuration. The example they gave was PRT_PARAMETER WIDGET STR EQ GREEN in one file and BLUE in another. After speaking with support, this will ONLY work if the "first three items after start tag (Mode) in the start item are same (WIDGET STR EQ)". However, if the two start files include PRT_DATUM PLANE 'name' 'number' and the name changes with the same number then it will not work. Modelcheck should be able to use the last start file and understand that the feature name will be different for the feature number and not flag it as an error - no matter what is listed, since it will be in violation of at least 1 start file.