The main difference I see with Seahawks & Niners defensive strategy is
Seattle loads up on bodies in the Front 7, while having their most skilled defenders in the secondary. We do the exact opposite. Our Front 7 has multiple All Pros, while our corners are just bodies.
This leaves us vulnerable against spread attacks. Being a power team gives us a clear advantage on offense but on defense it sometimes hinders us as this is a passing league. Most teams expect to be unable to consistently run the football, so there is always a backup plan versus the 49ers defense.