The cause for confusion is that there are two ways to calculate the base score.
Competition Manual Section 7.6 says containers in the tallest stack are not counted as part of the base. The base is simply all containers not in the tallest stack.
Rule SC8 says total containers in the stack minus the stack height are added to the base score, so some containers in a pyramid stack will count.
See an example at:
http://www.skene.org/robots/Final-Configuration.jpg
FIRST needs to decide which of these scoring methods will be used. If 7.6 is used, then there cannot be negative scores. If SC8 is used, then there can be.