Final itinerary. Which Swiss Pass?

With a Swiss Travel Pass in 2018, all benefits, whether covered or discounted, are available only on the counted travel days. You would benefit from using your pass for everything mentioned above, not just the train rides, so I'm not clear on where you were planning to pick and choose to use the 8 flexi days. You'd be better served to spend about $40 more per person to have 15 consecutive days of coverage and discounts.

GVA = Geneva airport (I had to look it up).
Yes, a Swiss pass covers all rail lines and buses in Switzerland except some mountain railways, including Geneva airport. All trains heading for Geneva from the rest of Switzerland stop first at "Genève", the station in the centre of the city, and then terminate 6 minutes later at "Genève-Aéroport", the airport station.

The official map of what is covered by a Swiss Pass is here: https://www.sbb.ch/content/dam/infrastruktur/trafimage/karten/karte-sts-pass-gueltigkeit.pdf
You can see "Genève-Aéroport" at the far left, just past "Genève".

My comment on your route is you are going: Zürich airport - Luzern - Appenzell - Mürren - Bern - Lausanne - Geneva airport.
Luzern is south-west of Zürich, Appenzell is north-east. You are doubling back through Zürich. And then you come south again, through Zürich again, to get to Mürren. See the map.
More logical would be: Zürich airport - Appenzell - Luzern - Mürren - . . . .

And Luzern - Appenzell IS NOT the Golden Pass route. Neither is Bern - Lausanne.
The Golden Pass route is Luzern - Meiringen - Interlaken - Spiez - Zweisimmen - Montreux. Which, if you do Mürren after Luzern then you will at least do the first half of that route.

Thanks Laura! We will switch to a 15 day consecutive pass.
Chris, can we not take Golden pass from Bern- change in Spiez- Montreux- Lausanne?

can we not take Golden pass from Bern- change in Spiez- Montreux- Lausanne?

Yes, the bit in the middle, Spiez - Montreux is part of the Golden Pass route. But that is the long way around. There is a direct route from Bern to Lausanne, through the lowlands, takes 1h12. If you just look up Bern to Lausanne, that is the route you get.
The route you suggest takes 4 hours.

Note that you can combine a lake cruise with a mountaintop excursion to either Pilatus or Rigi, and the boat will be covered on your pass. But the trip up Mt. Pilatus on the cogwheel railway and the cablecar back down are discounted, not fully covered.

You can see the full price for the “Golden Round Trip” up and down Pilatus (via boat, cogwheel rail, and cablecar) here:

https://www.pilatus.ch/en/discover/prices/

I do not have a link to the discounted price with a Swiss Pass. But you might consider doing the Rigi excursion (boat to Vitznau, cogwheel train to the top and back down to Rigi Kaltbad, cablecar to Weggis, and lake boat back to Luzern) instead. That whole trip is fully covered on the Swiss Pass.

Www.rigi.ch

We did the Rigi tour since it was covered on our Swiss Pass. I highly recommend it! Schilthorn and Chillon are also completely covered on the Swiss Pass.