Can you go on holiday outside Thailand while waiting for a marriage extension application to be processed?

I did it in the past with a re-entry permit.

You can if you get a re-entry permit, but better not. During that under-consideration period, IO would contact you for visiting your house or witness interviews (depends on immigration offices). If you have a plan to travel abroad already, don't forget to talk about your schedule out of the country with IO when you apply for your next 1-year extension. But be ready to be told 'stay'.