Merseyrail's driving policy won't state specific "normal braking points" though, it'll be much broader than that - if, as you say, step two is considered as defensive driving, which seems reasonable for an intensive urban system, then why would the policy specify step one?
I think I broadly agree with your comments, apart from this bit. There's a big distinction between a company's driving policy, which is general in nature, and the driving styles and braking points taught by instructors at specific locations during practical training. It could well be that a much more gentle approach than the policy dictates is generally taught on the approach to Kirkby because, perhaps, it's known that a train running to time will have a minute or two in hand.