Section 8.3.8 of the manual says yes.
Quote:
8.3.8 Control, Command & Signals System
The FRC robot control system has been designed to provide advanced capabilities for the ROBOTS. The system has been designed around an open architecture that will allow teams to easily develop custom software to control the ROBOT and add electronics and custom circuits to expand the functionality of the ROBOT. Custom circuits may be used to indirectly affect the robot outputs by providing enhanced sensor feedback to the cRIO-FRC to allow it to more effectively control the ROBOT.
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There are many rules specifically mentioning custom circuits. You really should know this already.