Good question.
Prior generation of the TRA had straight sheaves. Doo went to a variable sheave angle to allow for easier top-end shift out while still maintaining high side pressure at lower shift ratios. Top-end shift was a problem on older TRA's.
The wear you are seeing is more likely a product of the fixed position secondary clutch when combined with the variable sheave primary. This makes it not possible to maintain "correct" alignment through entire shift pattern. The older alignment spec (2008) put the belt in proper alignment at mid-shift, which I think is the best choice as this is where the belt spends most of its life. The newer spec (longer jackshaft, or shimming the jackshaft) put the belt in proper alignment at idle and eliminates the visible dog-leg in the belt that bothered so many people, BUT it also puts the belt farther OUT of alignment at mid-full shift. A floating secondary is the only way to address this....and it does seem to change the wear pattern on the belt.
I don't know if cutting the sheaves is the best answer (or if there is enough meat to make this reliably possible?). The newer TRA works much better than the older style. If a guy did cut the sheaves, then you get into messing with ramp angles to regain the shift characteristics given by the variable sheave.
I just live with the funny belt wear, it doesn't seem to shorten belt life. With proper setup, the whole combination works very good IMO.