The big, big, big question I have is: What if your mods are parts from other subarus?
Obviously turbo/exhaust etc leading to engine failure should NOT be covered.
But what about stuff like brakes? I thought I had front diff issues at one point (turned out I had crappy wheel spacers so i ditched them and bought the proper wheels). At the time, my only mods were my front seats and 4-pot front calipers. I talked to a subaru dealer employee and friend who had no idea which way his dealership would rule on the matter.
The way I see it is that I fixed a problem subaru had--they put front brakes designed for a 3000-3300 pound car on a 3600 pound car. There have been several brake issues reported on these very forums in this very section with the stockers. Still don't know if a diff replacement would've been covered. I'd venture 'probably not' due to the spacers, but without them, who knows?