It would be nice if large binary formats used e.g. tar as a part of their spec. This obviously doesn't address the current situation.
Perhaps something that does address the present situation is simply viewing files which have changed their modification date as changed and running a diff index in the background. If it were possible to transparently wrap the binary blob in a paged format then modification dates could be taken on each block/page. This seems to all be at the cost of the VCS trying to not inject itself into the workflow, possibly injection could be optional.