Could you explain a little more about what a dojo without a respectful atmosphere might look like? I think what you are getting at is that the sort of Cobra Mai dojo from the original Karate Kid where "THERE IS NO WEAKNESS IN THIS DOJO!" is the opposite of the respectful environment you are describing. But I think the difference between the iaido and jodo dojo you trained at and one where the instructors are displeased if the students don't bark "OSU!" properly is more a matter of where the formality sits in the training.
I think this conversation sort of moves into the realm of, some Japanese martial arts picked up these militaristic / nationalistic features at the front end of the 20th century and that became a part of their traditions. And also there's a thing about hazing people into a group in Japanese culture that exists in companies and schools.
Some examples of common disrespect may include standing when sensei is explaining something to a paired couple, standing with one's hands on one's hips, talking while a technique is being demonstrated, looking out the window while a technique is being shown, very junior students instructing their partners to name but just a few that I've noticed over the years and which drive me absolutely crazy whether I'm teaching or not.