The point limit sets the maximum number of points which will be identified in each photo during the Align Photos process. As cbnewham mentioned the number of points actually identified on each photo may be less than the maximum number set.
I have experimented setting the maximum number to 80,000 with High Accuracy when aligning 15Mp photos. I have not seen appreciable difference compared to a limit of 40,000.
With Medium Accuracy only 20,000 points or less are identified in each photo so changing from 40,000 to 80,000 does not make any difference.