So yes, annihilation refers specifically to any process that would at light speed render the universe lethal to life as we know it. I think of it sort of like living on a bubble that's always bursting (in timelines we don't observe). There's something left over but it's pretty unrecognizable.

Any account of the origin of the universe is probably going to have some anthropic consideration, so Boltzmann brains are not a unique problem. But I think fragile universe hypothesis may be an asset in solving it. Conventional cosmology calls for a short lived active universe with an infinitely long lived remainant after heat death. Whereas in fragile universe that remainent dwarfed in scale by the outcomes of these shattering events which may well create intelligences that don't suffer the Boltzmann pathology.