Just like understanding the call flow helps give the troubleshooting a logical approach.
Knowing the call flow within the gateway subsystems helps troubleshoot the gateway.
Cisco has some documentation to help on this aspect in the link below. You still might be able to fix issues without knowing how the voice gateway works. But that kind of skill is not transferrable or reliable in all situations.
The proprietary part of the technology should be the code. If there is a debug command for a subsystem then its necessary to know how that subsystem works. If even the working of subsystems is proprietary then there is no point having subsystem relevant debug commands published, because one would have only a layman understanding of its output as opposed to a professional one.
How can we use the debug commands relevant to the gateway subsystems with prudence if we dont know the basics of how they interact ? I take it that you may not have the answer to this question but it would be very helpful if you find and share this info. Like you suggested am already trying to work with what I have.
Here is a little excerpt from a cisco document published around 2006,
An important factor to consider before you start any VoIP troubleshooting or debugging is that VoIP calls are made up of three call legs. These call legs are source Plain Old Telephone Systems (POTS), VoIP, and destination POTS. ....
Troubleshooting and debugging needs to first focus on each leg independently and then on the VoIP call as a whole.