You do not need to book separate tickets to cross the Italy-Swiss border on the EC trains. Don’t use Trainline for this. On both SBB.ch and trenitalia, there is an option to enter your Half Fare card for the Swiss portion of the journey on the direct train from Como San Giovanni to Luzern. It brings the price on SBB.ch down to 41-44. CHF.
Also, do not need to book Swiss regional trains. Buy your BO Pass when you arrive in Luzern, as it will cover the train from there to Interlaken Ost and the train from there to Lauterbrunnen and on up to Mürren (including the cablecar segment).
The Bernina Express is well to the east and out of you way unless you are starting fromnVarenna or other town served by train on the east side of Lake Como. Maybe this map of the Swiss rail system will help. It does not show many towns on the east side of Lake Como but it does show how far east you have to travel to catch the Bernina Express.
https://cdn-doc.myswissalps.com/docs/default-source/rail-network-maps/swisstravelpass.pdf?sfvrsn=7788603a_56