Found a workaround. In Moodle I changed the SCORM Grading Method to Highest Grade.
(I was originally having trouble with Highest Grade because 3/3 was showing as 3% in the gradebook. Someone explained that I need to set the Maximum Grade setting (beneath Grading Method) to 3 in the Moodle SCORM settings. This fixed the gradebook percentages. Now when I score 3/3, it shows up as 100%. Maybe we could rename Maximum Grade to Possible Points.)
This still doesn't resolve that the certificate doesn't work with SCORMs with Grading Method set to Learning Object. For me, this is no longer an issue. For others, it may still be an issue.