Are we allowed to have pieces permanently protruding from the robot, outside the robot base frame, as long as the pieces are inside of the perimeter parameters stated in the rules?
Yes. That is fine. There are no rules saying your mechanisms must be within your robot’s base.
As long as your robot follows R3 B, you are fine:
B. the ROBOT must be able to be arranged into a TRANSPORT CONFIGURATION with dimensions which do not exceed 28 in. wide, 42 in. long, and 78 in. tall.