No, you're not off base at all. Against a typical Cover 3, you'd generally try to attack the Seams and the Flats as you said. This is where Fred Warner changes everything.
SF doesn't take away the middle of the field by clogging it up with a ton of 2 High looks. C3 works for them because they have an alien playing MLB. It would not be hyperbole to say Warner enables Ryans the way Derrick Brooks enabled Tampa 2 to be a scheme base. Warner's unique ability to get depth so quickly means the other players don't have to worry about the usual gaping hole over the top of the LB this usually creates. Their rules to me look like they typically assume Warner gets there.
Everyone runs Dagger off of PA, but the Eagles love it. That's a great C3 beater too. For those that don't know, Dagger basically means your Slot runs a Post/Go to clear the way for your outside WR to run an in-breaker behind him in the 15-20 yard range. Time and time again, Warner manages to both hesitate long enough to make sure it's not a run and then get the necessary depth to get to that in-breaking WR. There's no more DB conflict because Warner replaces one.
As far as schematic similarities, I don't think anyone is a good comp. Even the Jets use a lot more Nickel than the 49ers do now. Of course no one plays C3 as often as the old Seahawks teams did. You can't just play one coverage that much anymore and expect it to hold up. They play a decent amount of C2 for example. They're not particularly good at it, actually. If the Eagles can force them into more 2 High looks, that's a GREAT sign to me. When I think of what SF does best, it's play with 3 LBs on the field.