I agree with you that graphics and sound mods have the potential to conflict with gameplay altering mods, and an MGSO user needs to know how to deal with that or avoid it through mod selection, or they will run into trouble.
As to your earlier point about credits, I agree MGSO needs a good readme that is included in the download that includes a good credits section. There is a credits webpage somewhere with a list, but it's hard to find the page and the list does not contain enough information about who contributed what. It's just a list of names.
It would be better if MGSO promoted its contributors.

  I don't disagree with the points you just made. You can use it as a base but you are right that it is trickier not only because of the "black box" but also because MGSO edits some of the plugins, so they are not the same as the originals, which means you have to be more careful when making changes. 