When I print using the default template only the answers submitted or selected appear in the printed form. But when I print using my own custom template all headings print even if nothing was submitted for that question. I even uploaded the default form created by Survey123 and uploaded it as a custom report and it acted just like my other custom reports and not the default report. It printed all headings even when nothing was submitted for those questions. Is this just a limitation to the Report (beta) option?
Yes, this is a current limitation of the report (beta) functionality. If you include the question in your template, the label for the question name will be displayed even if there is no answer.