You get unwelcome outcomes when you have over-simplified constraints. For example, if you are told by DfT "no additional costs" then you can't upgrade platform lighting and you can't hire more drivers. Sure, you then lose income (from cancelled services) or have additional costs (due to having duplicate rolling stock leases), but those factors weren't in the "no additional costs" part.
On a more concrete example, I talked with one of the SWR managers last year about removing a parking space outside Tolworth station, to add additional bike parking. They said that wouldn't be possible, because they can't make a change that would decrease the income from the car park. I asked if it would still be worthwhile, because instead of one fare for the driver and one payment for one car parking space, you could get six fares from six people arriving by bike, and that would be more revenue overall. He said that's not how it's calculated, the revenue from the car parking is considered in isolation, and that revenue must not be reduced. So I'm not surprised when stuff like this happens. Everything is siloed, and there's very little big-picture thinking.