Yes, for 40 minutes you are obligated to pay for a nude massage at $60 plus the $50 door fee for $110 in total. But if you ask them to keep their clothes on that's up to you.
You should go in thinking that you are generally wasting a girls time if you choose a fee that is less than the posted NR rate for that length of time. Also, some of the girls don't like the 40 minute session as it's 10 more minutes of their time for the same fee as the 30 minute sessions. Add another 10 minutes to 50 minutes and they would have pocketed another $20. But instead you come across cheap as you took the lowest option for the maximum amount of time before the fee hike kicks in. Now, you can choose any option you want that is posted and pay accordingly. However, you may find a cold attitude if you choose less than a NR at any duration.
Wasting the attendants time really depends on the attendant. If you booked a busy attendant and took a lessor option then you did waste her time as the other guy that could have booked likely would have paid more for a NR, BS or shower massage. Now, if you got an attendant that usually only gets a couple of clients a day you are actually giving her some money that she otherwise would not have earned you may not have wasted her time. However, her perception is what's important as she may still feel it's a waste of her time and would have rather not earned anything. It's the price that she's determined in her own mind for doing this job what is key and how to make the maximum amount of money each day without crossing any limits (hers and/or the spas). This is often implied as being the NR rate at the minimum.