In looking at the current itinerary it does not state that the tour visits the National Museum. However, it IS listed under the “Here’s what is included” section. The day you walk thru Grassmarket and go to Greyfriars Cemetery, that is just across the street from the Museum so they may take you across and get you started. I am sure on my pre-Covid Best of Scotland that is where we saw it.
I’ll add that since you are going to be there ahead of time, I’d visit then as well. Often the tours don’t spend as much time as I’d like in museums and churches so I go on my own. I have a 2-3 hour museum max so even with 2 visits I did not see everything!
You can call the office to see what the specific timing is for Day 11.
This is a big museum and filled with an enormous range of things. I’m going in 2025 prior to a return trip to Orkney to see some of the artifacts they’ve dug from the Neolithic sites on the island. I’ve got the museum map bookmarked (insert eye roll here) to study before my trip. The purple end where the Scottish stuff is, is the closest to Greyfriars and if I remember correctly we entered that way.
https://www.nms.ac.uk/national-museum-of-scotland/plan-your-visit/museum-map/