Just a feeling I have gained over the years from reading MT. I could be entirely off base. Then again, if I am right, it's hardly something anyone would admit to.
I think that it is fair to say that some, perhaps many, believe that a Kukkiwon certificate is superior to a dojang only certificate, but again, that is distinct from the student/teacher relationship. Now, the certificate does not imply that the holder is in any way superior, but the certificate itself allows access to things that a dojang certificate does not.
As I have said previously, if you are practicing Kukkiwon material at a school you attend, and the instructor is a Kukkiwon sadan or higher, then he or she should be issuing Kukkiwon certificates. That would include schools meeting the above criteria teaching palgwe pumse. As Glenn likes to say, give the same certification that you received.
To a great degree, the value of an organizational certificate varries from person to person, based on their goals. If all that I want is to earn a black belt and then move on (something that many people do), then a dojang dan is as good as an organizational dan. Sometimes, though, peoples' goals change and they find themselves in a position where an organizational cert would be of benefit. So,
if you train in a school that has organizational affiliation, you should
at least have access to the organizaitonal cert, though frankly, I believe that schools with organizational affiliation should be issuing organizational certifictes.
Daniel