I see. I expect they should be flush all the way down. Mine are flush at the lower corner of the tail light but the tail panel protrudes by a couple of mm outside the quarter panel at the bottom. Kind of like yours would be if the tail panel was shifted left by a couple of mm, or the rear quarter shifted right. Maybe you could test fit the tail lights in the current configuration. If the lights fit well and that small fender to tail panel discrepancy is symmetrical both sides, it's probably fine like that. I had never noticed mine weren't quite aligned until now.