You don't say what type of dog you but but I get the impression that he's not a small dog.
I have a small, very laid back, dog but if something spooks her when she's asleep in the garden she will do exactly as your dog did: growling, barking, her whole body ready to move, it's what a startled dog does.
There's a very good reason for the expression 'let sleeping dogs lie'.
You dog was in a strange place, having a doze. Her sudden knocking would have really surprised him and he probably did look scary, but he didn't actually do anything other than bark and growl; growling sounds mean but it isn't anything more than a warning that a dog is not happy with the situation.
It sounds like you're more than able to cope with him, you took him out of the situation without him reacting. A really wound up, out of control dog wouldn't be so calm about being handled and remove to the bedroom.
I agree with pp, it's not necessary to ring the owner of the cottage and apologise again, you've apologised already.
She's was probably a bit shocked at your dog's reaction but tbh if you know there's a strange dog in the cottage it's a bit silly to go knocking on the patio door and then be shocked when the dog reacts, as most dog's will.
Might be an idea to have a word with your vet about calming medicine for him when you get home.
Try to enjoy your holiday.