Interesting to hear D2L have done it that way (I haven't seen this in other SCORM players myself) - in Moodle a SCORM package is a stand-alone object and the reports within the SCORM package show the information returned about the package but we only push a single grade for that package to the gradebook. To do this differently would require a significant amount of development and I'm not sure that it would be worth the effort.
The easiest way to achieve a similar outcome in Moodle would be to separate it out into multiple SCORM packages and then improve the behaviour of SCORM when a user exits a package to allow them to automatically open the next SCORM package or return to the course homepage. I'd do this by adding a setting to allow the teacher to decide what happens when the user exits a scorm package for example - return to course homepage/dashboard/another activity in the course. This could also help to resolve MDL-44905