You're observations are correct. In most respects, the ECOM100 is treated as a legacy device, so ...
Both the MRX and MWX instructions are limited using the onboard serial and Ethernet ports, and DLRX and DLWX instructions can target an ECOM100 but they can only use the module ID.
We do have plans to change this behavior and allow the ECOM100 to perform most of the functions that the onboard port can.
Can I ask why you need to run Modbus comm (or DL comm) through the ECOM100 module and not the onboard Ethernet port? If you are trying to segregate traffic between HMIs, C-More panels and such, can you use the ECOM100 for DmDesigner programming and HMI access and use the onboard port for Modbus comm.