Hello Alek
Provided you have FIP reduction valid for FS/SBB:
Either purchase a through-ticket Milan-Spiez with FIP from Trenitalia. This is valid for the travel form Milan to Spiez. It includes a seat reservation.
Or, you split the tickets: Milan-Domodossola / Domodossola -Spiez. When doing so, for the Swiss part, you can purchase a ½ fare ticket Domodossola - Interlaken. It does not include a seat reservation, as regular and international trains do not need a seat reservation in Switzerland. You simply continue on the EC to Spiez.
No matter if the companies do cooperate (and yes, they do), the tickets are independent from their cooperation and have to be valid on the respective network and carrier.
The RE80 is operated by Trenord on the Italian network (not FS), thus your FIP would need to be valid for Trenord, too. And even there: you need a ticket for the Swiss part that is accepted by SBB, and you need a ticket for the Italian part, accepted by Trenord. Whether this is one single direct ticket or two tickets is secondary, depending on the offer available.
Sometimes it is easier to book a regular (or saver) ticket rather than using FIP.
For example, to Austria, I never use FIP. A supersaver ticket is less costly and I even do not have to bother with FIP, discounts, acceptance, and so on.
Kind regards,
Roland