I'm honestly not sure if you can open the same Channel more than once at the same time. I'm not sure it matters, because each Channel definition file hard-codes the IP and port to be used, so unless the remote computer has some very unusual network setups, it's probably a moot point.
IIRC, the EKI manual says you can have up to 3 EKI Channels open simultaneously. So as long as you are using separate Channels, opening different IPs and/or ports, running one in the Robot Interpreter and one in the Submit Interpreter should be fine.
You do need to make sure you set up your Channel config files correctly, though. For example, an EKI channel opened from the Submit should be configured to automatically close if the Submit is cancelled. Otherwise, you could leave a port "dangling" in an open condition and have no way to fix it but rebooting the robot.