AT command interface is accessible in the /dev directory. This varies from device to device, but at least on my RUTX50, it is mounted on /dev/ttyUSB4. This can be checked by using the microcom tool, which is pre-installed on our devices, and connection to the AT interface is possible using the command
You can check if you connected to the correct port by typing ATE1. If an OK answer is received, you have connected to the correct port (echo will be disabled before and after sending the command, so you will not see what you are typing). Would this approach be suitable for you?
If not, there is also USB over IP software available, which could make the AT port accessible directly on the VM manager, however, this would introduce the same issue as simply using the RS cable.
I'm not sure how your application works exactly, so I'm not sure what other solution could I recommend. As I understand it now, you are receiving pure AT commands from another software, and are basically forwarding those commands to the RUT956 with the gsmctl layer attached, is that correct?