The option to include or exclude empty grades is based on the Gradebook categories so if you wanted to have both you could add another category and have the option ticked or not and include the appropriate grade items.
As mentioned though this is adding a layer of complexity to the gradebook which maybe difficult to manage depending on the number of Courses.
Either way an explanation to students should be clear in that their final grade is an interim grade until all course assessment items have been submitted (or not) and they need to look at the overall assessments and the weightings (if used) when looking at the course grade.
So to do the opposite as you have you put a tick in the parent category to 'exclude empty grades' which then shows the student their current course grade based on the assignments they have submitted. This of course could show the student has a HD but in fact the last assessment item has a weighting of say 60% and say they get a pass for this one there overall grade would drop.
Personally I prefer the latter as it gives a 'current state' of the overall grade but it does mean that students may look at this and 'slack off' for the last assessment because they only need a pass to get over the line in the course.
Hope the above helps in what is a mind field!