I don't think this really is about naked or not naked, hygienic or unhygienic. Its about how your dad will react to your child doing something "wrong", whatever it is. It sounds like he was uncomfortable communicating that he didn't want a naked toddler sitting on his furniture, perhaps because your mum and you were automatically so OK with it. He held this discomfort in, which upped his stress level. This led to him snapping and shouting at your child. You need to discuss three things with your dad:
1. How if he is concerned or uncomfortable he needs to talk to you rather than your child, and you need to promise him that you will hear him and take his feelings on board
2. Describe the methods you use to communicate with your child when you need to discipline her/dissuade her from doing things
3. Explain that you don't expect him to be perfect - that you know from experience that parenting (and grandparenting) is full of mistakes. Explain that you as an adult can understand why he snapped but your daughter can't, so she will blame herself, and he needs to apologise to her.