I'd stick to whatever your guitar is supposed to use. I doubt a slight deviation is going to make any difference. None of my guitars' spacing was lined up perfectly. I don't think I've ever seen one that was.
My vote is 50mm for a les Paul. I have heard tonal differences between 50mm and 53mm, may just be pickup variations, but it was significant. So much so that I would not get a 53mm JB pickup again, but would a 50mm