I believe you're worrying too much. Some advice :

Seat reservations are not a thing in Switzerland. They are not possible on regional trains everywhere either (for anyone, whether you have a ticket or a pass). Where did you find that a seat is required ?

Interlaken Ost - Grindelwald is indeed not included but you get a 25% discount which is better than nothing. The discount also applies to some mountain railways and cable cars in the area. No need to use a pass day for the discount.

Boats on Lake Thun and Brienz are fully included so do take them :)

The only mandatory seat reservations I see on your itinerary are : Paris - Strasbourg (done), Milan - Vernazza, Pisa - Amalfi and back to Rome. Availability in Italy is never a problem so you can literally decide on the day which train you'd like to take.

More info about the pass : https://www.seat61.com/how-to-use-a-eurail-pass.htm

In order to travel and get a QR-code (your ticket) you need to add to Rail Planner app each train you'd like to take (log the train). This can be done at any time prior to boarding.

Thanks for the quick response. You are probably right, that I’m worrying too much. Nervous Nelly here. But we are traveling with friends who are following my lead on these purchases and I hate to be doing the wrong thing for them as well. 

One of the main reasons that I bought the pass was that I thought no more purchases would be required except for the ones with the seat reserved requirement. Therefore making it very easy to move around, by just having the pass scanned But it now appears that we will have to purchase tickets for everything in Switzerland, therefore the cost effective aspect pretty much disappears.  Having to make seat reservations on Milan, Pisa, Rome legs eliminates the ease and impacts the overall cost effectiveness.

Do you know if we can get a refund after activation and cancelling our first leg? 

Thanks, 

As long as you haven’t started using it you can apply for a refund, there is a 15% fee on the purchase cost.

Details here https://www.eurail.com/en/eurail-passes/ordering-info/refund-exchange-policy

Before you ask for a refund you should check what the cost for normal tickets for your travel will be. As you are travelling rather soon I guess that the cost will be higher than using the global pass including the extra costs. 

Well you understood correctly : you have full flexibility in Switzerland and where seat reservations are not required. The only thing you need to do is log to the app each train you'd like to take before boarding. It's easy, don't worry.

The only discounted tickets you may need are Interlaken Ost - Grindelwald (and in that area). They can be purchased at all train stations of the country and maybe on jungfrau.ch. Tickets cannot sell out and are valid all day on the chosen route (= flexibility here too).

Now in Italy you'd only need seat reservations on the fast and high-speed trains and as I said it's not an issue : they run every 15 min between Florence and Rome for example. The requirement is written on the app. If you found R/RV regional trains on your itinerary then those do not require reservations (it's not possible anyway).

Make some calculations but I'm pretty sure that the pass is a good deal.

Just for clarity - the majority of trains operated by national rail operators and some private operators (e.g. Eurostar) are included in the pass. In several countries there are indeed extra charges for reservations but in most cases these are for sleepers, high speed trains and long distance and cross border Inter City trains.

Currently there are operators appearing similar to low cost airlines (several owned by the national operators) that are not members of the Interrail partnership, but these are clearly indicated in the IR planner and there is almost always an Interrail option.