The three boards on the EOB motherboard are all Lionel standard boards, the R2LC, RS4 Audio, and RS4 Power Supply. All the EOB logic and drivers are on the motherboard.
You could try disabling the cruise capability, I haven't actually tried that with an EOB board yet. From the manual, it appears it "sticks" through a power cycle.
Instructions from the EOB Manual.
For the Cruise Off mode;
ENG + ## + DIR + AUX1 + AUX1 + AUX1 + 3
(The horn will sound after the 3rd AUX1 and after 3.)
The Cruise Off mode will provide 100% lash-up compatibility with non-cruise equipped locomotives. In this mode the response to commands is exactly the same as any other command equipped locomotive without cruise control. You do not need to reenter the command at power up unless you want to change the speed step modes.