Some other roads had local companies which were part of the "System". Some of these were caused by local or state laws. SP had T&NO in TX because of state law. Gulf Coast and Santa Fe was begun and owned by Galveston County. It connected with the ATSF in southern OK. ATSF bought it, but kept the GC&SF company organization. My guess the same TX law which required a RR in TX to be a TX based RR. This law was removed around 1960. SP merged T&NO in the early 60's. I do not know what ATSF did.
Second, some companies, including railroads had poison pills against any sort of merger. So you bought it, intergrated operations as best you could, and left it alone.