in early 2020, when travel was easier, I flew to Australia while my extension of stay (Non O married to Thai) was under consideration. I had to go for just a few days. I got a re-entry permit and it all worked fine.
Now that travel is a bit more difficult and dates are less reliable, I'm not sure if I would try. But it did work then...
I managed to do mine online OK this week, after doing a new extension of stay early in the year and a 90 day report in person while the website was down. Lucky I guess.
I'm sure when they first introduced the 60 day visa, one of the published rules was that it could not be renewed OR an application made to change to another visa. Of course this may have changed...
My last one showed as pending for over a week. When I went back to look again, 5 mins after I'd last looked, it was then approved....seemed like the system needed a 'nudge'?