I've refurbished upwards of 500 MacBooks (old employer bought MacBooks in bulk from school systems, refurbished them and sold them) and I can say the only way to get the absolute perfect alignment is to replace the hinges, which are relatively inexpensive at $40/piece through iFixit.
With that said, I've ended up with "not perfect, but not noticeably off" results pretty often just by applying pressure to the display. I've seen one LCD crack when doing this though so be cautious with your actions, I assume no liability for damage stemming from my suggestions.
With the MacBook sitting on a grippy surface (ESD mat usually), with it's display closed, I would push the display to the left or the right (depending on the misalignment) a half inch or so and hold it in place for a minute or two. This is almost a twisting motion. After several (5+) rounds of this I would usually notice the misalignment becoming less and less noticeable. I imagine if you could find a way to hold it in place for 30-45 minutes that would do the trick as well, I just never found a good solution for doing so.
Hopefully this works for you!