Connect two different sources with two Digital Ouptuts using an Adam 4055
I am answering my own question because I think it fits better than updating the question. Feel free to comment I update the post accordingly if it does not suit the EE.SE guidelines.

As @dim suggested, I have contacted the manufacturer and I have received an answer. The IC inside the Adam-4055 driving Digital Outputs is a ULN2803 (specs, info). The reason why they connect the D0.COM pin is to take advantage of the built-in the fly-back diodes.



The Open Collector gate is a Darlington:



According to this new information, I think I can:


Share the D.GND pin among power sources;
Skip the D0.COM pin and miss the built-in fly-back diodes;
Use different power sources (within the IC specification);
Add additional fly-back diodes on inductive loads to protect the IC;
Add Optocoupler if I want to completely isolate loads from IC.


A possible setup is now (I may have not chosen the best symbols):







simulate this circuit &ndash; Schematic created using CircuitLab

Now it is just about shipping compliant components provided they exist and are available. Thank you for your valuable feedback.