Those level indications are slight, and could be just errors in parallelism or tool alignment. Crushed downtubes are common for the reasons you mentioned. Usually the neck is checked with a long rod centered where the steering stem would rest in the neck and the frame leveled. Plumb bobs can be dropped from each end of the rod and then compared for alignment with the frame. If it is twisted, there will be some wrinkling, dents, or twists, however subtle, somewhere. Wrecks normally produce a center of impact with twisting stretching or crushing of the surrounding area. Did you hold the handlebars lightly when the bike pulled? Some riders have a tendancy to try to pull bent or twisted bars straight, without even realizing it, thereby introducing a pull.