So if I'm understanding this correctly, when you rotate the pinion back, the track bar is getting "rotated" along with the axle and then interfering with the gas tank. I'll be honest, I've never messed around with my rear track bar personally, but to me, it would seem that the mount for the track bar on the axle side should be on top of the axle (or at least the track bar should be parallel to the axle). I would think you'd have to relocate the axle side mount forward, moving the track bar forward. If you moved the frame side mount forward, you'd have a pretty good angle on the track bar relative to the axle.
Again, this is just wild speculation on my part because I've never had to do it myself.
Correct. If you rotate the pinion back (or upwards) it's causing the track bar to be rotated back with it. This is causing the upper portion of the rear track bar to contact the fuel tank skid. If you did what you are describing though and had the axle side bracket for the track bar facing straight up (instead of the angled bracket that it has now), then you'd bring the other side of the track bar more in contact with the gas tank skid as well.