When a feature class has an established relationship class with a stand alone table, the editor must have the same edit permissions on the table as they do the feature class or they will not be able to edit the layer.
Based on this reason alone, tables should be allowed to be placed in a feature dataset so they will have the same edit permissions as the feature classes that they participate in the relationship class with.
I agree, my database is getting messy and confusing because I can't house it all under one feature dataset.
Nearly 11 years laters, and a folder display/managing system in the .gbd still not implemented. And people will still fall into the resource hog trap of using FDS to organize.
This would still be a useful feature. How else can layers be grouped in SDE easily?