Think of it as speaking a foreign language. If you went to Spain, you would need to communicate in a way that people there understand wouldn't you? Think of communicating with neurotypical people as being in a different country. Their language is has the same words but convey meaning differently based on tone and a bunch of other stuff.
In case of the dogs, the neurotypical communication carries information regarding how much fault you assign to that person and yourself, whose stakes are higher, what is the expected action, what are the possible consequences of not doing that and so on entirely in non-verbal format, something that we have trouble with.
The could you and thank you part is essentially communicating that you're acknowledging (and in a way probing) that they didn't probably commit the act out of malice or neglect and giving them room to communicate, while also indicating that they would be helping you by not letting it happen.
Now I am not great at emulating light tone or the correct expressions so I usually just say all of this explicitly in my normal tone. That seems to work mostly.