Have you been to Switzerland before? The Best of Switzerland is a fantastic trip that really shows a traveller how beautiful the entire county is, and plants the seeds of desire to return- several times. We did that tour in 2017. However, you do spend a lot of time in cities- beautiful cities. The tour does traverse through countryside with spectacular scenery. Do you want a Swiss country tour or a hiking trip?
If you do the BOS tour, perhaps come in a day or two early to Luzern, and go up to Mt Rigi and/or Mt Stans to hike. [The Swiss Travel Pass covers the boat and cogwheel train to Rigi, and the train to Stans.]
The Berner Oberland [and staying in Murren] is fantastic for hiking, but two nights is just not enough time, especially with mountain weather. Having been to Switzerland three times already, I'd almost recommend returning to the Berner Oberland at the tour's conclusion- it's just an hour train ride from Bern. Maybe stay in Wengen to experience both sides of the valley.
Our 2017 trip didn't include Appenzel, but I'm assuming there are many wonderful hiking opportunities in that area.
Lugano wasn't my favorite place; it's a very high-end city on a lake.
Lausaune was charming, and the wine tasting and Chateau Chillon made a great day.
You have all good options, so have fun planning an incredible trip.