Hello UW Dawg
Welcome to the SBB Community… Here in this travel forum, we are volunteers helping other customers.
Your itinerary includes unnecessary backtracking; why going back to Zurich for the train to Como? You could well travel Zurich to Interlaken to Lucerne to Como without travelling a single stretch twice.
Yes, the Swiss Travel Pass and its Flex version offer both the option for class upgrades, and this either as point-to-point class upgrade or day class upgrade. When doing so, choose GA 2nd class as reduction type as Swiss Pass holders do benefit from class upgrades at reduced fare.
For the train to Italy, you can book a 1st class ticket with GA 2nd class reduction type. Or use the Swiss Travel Pass for a travel to Chiasso (border station) while you purchase an Arcobaleno Transfrontaliera ticket (only valid with RE trains) from there to Como for little money. The train change can still happen legally at Lugano station already.
Seat reservations are not necessary for trains in Switzerland unless you are required by the operator (e.g. Glacier Express). Our trains are mass transit: hop on, find a free seat, hop off.
Note: Instead of the Swiss Travel Pass, the Tell (Lucerne) Pass, and the Berner Oberland Pass could both be a viable alternate. The Swiss Travel Pass is not very useful in the Berner Oberland.
Or, simply purchase the Swiss Half Fare Card and individual tickets as you go. A Swiss Travel Pass travel day might be more expensive than the actual single ticket. You should do the maths using a spreadsheet.
A little side note: for a Swiss, being asked a question without a preceeding hello or thanks appears very odd. Swiss love niceties.
Kind regards,
Roland