Can I leave Thailand while my Non-O marriage extension application is under consideration?

As was stated you can ineed leave/come back during the under-consideration period on a yearly extension if you buy a new re-entry permit (which will be valid only during that stamp) 🙂

As was also pointed out you need to talk to your immigration office when you apply for your extension to see if they are going to do a home visit during the u/c period.

You need to coordinate that with them