A couple of thoughts.
If you are interested in saving money on your accommodations, consider taking an apartment for a full week in Mürren (or possibly Wengen). Chalet Bobs is highly recommended, although we've not stayed there ourselves. Apartments usually rent from Saturday to Saturday, although September may be off-season enough that they will make an exception. If not, you could adjust to that by going to the BO first, staying 9/11 to 9/18, then heading to Zermatt.
Yes, this would change your plan to 7 nights BO and 3 for Zermatt, but I have a higher opinion of Zermatt then others have expressed here, especially if you are hiking. With 3 nights there, you have 2 full days to explore the hiking. One of my favorite hikes in Switzerland (and we've hiked all over there, both in the Valais and the BO) is the one to a mountain restaurant called Fluhalp, past the Stellissee (lake) which is famous for the reflections of the Matterhorn across the valley. Gornergrat is also a fantastic spot, with views comparable to the Jungfraujoch, but you can hike all the way up there if you like (or take the train up and hike down (as most people do).
As far as your flights, you can fly into and out of Zürich. The train trip to or from Zermatt is shorter from Zürich (3:19) than from Geneva (3:45).
For your train pass, you have to "do the math", but I have found the best option for a hiker staying in 2 different places is the 3-day Flex Pass, Saver version. A "saver" pass is just a pass for 2 or more people traveling together, with a 15% discount for each. The Flex-pass functions as a half-fare pass on the days between first and last use. So use your first day for Zürich to BO or Zermatt, second covered day to travel between BO and Zermatt, and third day to head back to Zürich. All other travel (which won't be long trips, just short hops for hiking or sightseeing) will be at half fare.