Hello Kai,
I'd like to know – what is your initial problem that you cannot solve through the GUI?
VDSM does use a custom comment in ifcfg files, but only to recognize them – if they are unknown, it acquires the relevant network devices from NetworkManager. But VDSM is in charge of networking configuration, exclusively.
If you need to add extra configuration parameters in ifcfg files, or modify them, you could write or use a VDSM hook to alter the ifcfg files as they are written.
But perhaps it is better for us to know what problems you are having and whether they can be solved by available methods.