Reference parts are great way to model your sub assembly being able to see the context where it lives. Then when you insert your group in the whole machine you no longher need these references.
It woluld be great to have, at least as an option, the possibility to have references hidden or suppressed by default. This will help in keeping big ena complex assemblies light and fast in memory.
Actually we are doing it with LOD or view representation but the designer of the group need to specify reference parts and create the LOD "NoReference". The automatic way is faster.