Tour premission Myanmar is usual in Myanmar while you are traveling especially countryside. There might be several check point that you need to show your passport but you are secure all along your travel in Myanmar. It is only because
Myanmar government doesn't want any trouble with tourist or visitor in Myanmar. Myanmar authority checks your permission paper or pass port why you are traveling is only for your own security reason. Information about when and where you can go some unseen Myanmar area is not sure. Some travelers arrange with group tour permission Myanmar for their trip. Even though you have permission to travel some places, they will check you all the time on your trip.
Make sure your visa is valid if you are traveling Rakhine state region and Shan State as there are numerous passport check points. Nothing happen even you over stay but authority might send you back to Yangon for visa extension. Staying at the beaches in Myanmar is safe and you can over stay as long as you want just need to pay 3 US$ a day when you depart the country.