I was thinking about this today while I was driving and I think there are two separate issues being discussed on this thread. The original is the wrinkled skin and crimped brake lines. The second is the bolt and channel cracking issue. I think they are probably unrelated.
The channel is one of the beefiest pieces in the fuselage, basically a 1/4" C channel. It will probably be the last piece to actually bend, but the surrounding structure is not nearly as strong, especially the part of the fuselage attached to the rear side of the channel. I noticed that all of the wrinkled fuselage pictures show a vertical wrinkle, as opposed to a horizontal one. This supports the hypothesis that the rear part of the fuselage and tailcone are actually moving in a downward direction. This would push the side skin below the channel forward where it contacts the brake line. The baggage floor attach point to the channel acts like a hinge to allow this. If you think about it, everything above the floor of the baggage compart has very little lateral support, especially above the longeron, since that is where the rear window is. These skins are thin! (.020 or .025 if I remember correctly) Even in a monocoque configuration, even though they are very strong, they can still fail. Like an aluminum can, if you bend it a little too much. Maybe it's aerodynamic force, too many heavy landings, rough fields and heavy braking or a combination of all of these, but I personally think that the rear fuselages are just bending down causing the wrinkling. Maybe a diagonal support from the channel to the rear and up to the longeron would help, I don't know. The fix is for VAN's to design.
As for the channel and cracking bolt holes, maybe it's just a metallurgical issue with some of the parts, or maybe some of the bolts are getting over torqued, I don't know, but I see it as a separate issue from the wrinkling.
Just my observations for you to think about. I hope someone figures it out.