I have been on this tour. It is possible to skip a portion, just consult with the guide to fond out where & when the group reconvenes so that you can catch up with them again. It is probable that after Versailles there will be a bit of free time; on my tour, we all returned to Paris on our own, with our ticket paid in our pocket. So some would spend more tome on the grounds and others return back sooner. I had lunch in Versailles with some tour members and returned mid-afternoon. During the Paris city tour, I did skip a group activity to go the the Orsay on my own, as it is my fave museum.
I really enjoyed the Paris city tour. I was glad that I had booked 3 additional nights on my own after the tour, just to wander along the Seine, or do some shopping. One of my favorite things to do in Paris is to visit the markets, which I did after the tour ends as they are usually morning markets ending about 1 pm.
In my experience, the group stays at the same hotel for all nights.
I toured the Army museum and did like it. The gardens are fabulous. I did return to the gardens only to sit in the sun.
Enjoy. Paris is my favourite place in the world. I have returned at least 4 times on my own and with freinds.