"Is it an etiquette rule that you shouldn't flush at night while a guest?"
and I guess
"Can I expect a guest to not flush at night while they are a guest?'
My personal answer is No and No.
While I agree that you can say No to both of these, if you were a guest in my home, I would have to reconsider whether or not to invite you to stay overnight if you kept waking me with flushing at night. Sleep is more precious to me than waking up to a flushed toilet.
Just as you, as a guest, has the option not to visit someone who insists on the toilet not being flushed every time.
I would never insist but waking me in the night ensures you'll have a grumpy Outdoor Girl in the morning. When I'm wakened, it takes a long time for me to go back to sleep.