In addition to making sure the property is set, samigo.autoSubmit.enabled=true, one also has to run the quartz job manually (or set up a cron) logging in as admin.

And also one needs to run auto submit oracle or mysql insert statements https://github.com/sakaiproject/sakai/tree/master/samigo

Seems like that is what it took. It's possibly to manually add this auto submit option to the default template type as admin, but probably easier to get these scripts run.

You will know the setup is working if you see the auto submit option under Settings (see autosubmit_option.png for screenshot).
Here is what I did:
1) Set up a simple two question exam as instructor.
2) Choose settings. Set Due date pretty soon (with 5 - 10 minutes ) . Set Late Submissions (aka Retract date) to 5 minutes past the Due Date.
3) Set up an exception for 1 student to have a due date of a day later and late submission 5 minutes passed due date.
4) Take the test as 2 students but don't complete for either of them. 1 of the students must be the one that has the exception of tomorrow. Make sure at least one of the answers is saved, if not both (I just find it interesting to see how an unanswered question is handled.)
5) After the Due date for the class (not the exception) but before the Late Submission / Retract date, run the Auto Submit job as admin.
6) Check as instructor that no exams have been submitted. Works correctly.
7) Wait till after the Late Submission/Retract date. Run the Auto submit job as admin.
8) Check as instructor if any exams have been submitted.

Expected results: The student with the exception should not have had her exam submitted, the student without the exception should have had the exam submitted.

Repeat the test, using a group instead of an individual student.

Actual results: Both students had their exam submitted. Incorrect behavior.