Actually I think the drivers probably don't know why the runway isn't flat either. Better ask a civil engineer !
Seriously it's the sort of thing that happens with incremental lengthening of a runway. Originally it would be either level or at least on a constant gradient. When extensions occur (and the main runway at Manchester had a lot of these over the years) maintaining the constant becomes impossible when you extend over a hilltop and down the other side (which is what happened at Manchester). What was originally a runway under one mile long that fitted into a site has ended up as one over two miles long.
With the new runway there was no history to tack onto the end of and they could start again.