How do I attach twist straps to rafters along the top plate?
Just tap the toenails in deeper. Use a finer tipped chisel if you need to. Then attach it as the engineer has specified. 

Even if the wood is rather old, the direction of the force that the nails and bolts are acting in shouldn't rip it apart. It'd be noticable if it was dangerous from your photo and that's not the case.