I'm running a flip/flop hub right now, and I've had this frame for many years. It's gone from the original 10 speed, to a single speed, to a six speed, and now fixed (Rather than buy new bikes, I've always just changed this one). I'm actually going to turn it back into a six speed now for commuting, which led me to noticing this issue. Never noticed it before, and can't remember being hit by a car or anything...
I checked out the Sheldon method first (don't we all?) and the measurements are fine, so I don't want to mess it up by tweaking the chainstay angle/spacing.
I think I'll try Sheldon's 2x4 method with a hub in place. Hopefully, this will keep the spacing intact while moving the thinner seatstays back into place.... right?