It might be assumed that the writer referred to in FHSoc's post is an LBL representative.
On the major items it may be the case that the list does not refer to problems with track bed drainage and that contingency sums might be to narrowly focussed on what might be misunderstood to be surface water issues within the subway.
It may also be the case that at the time of major track works over the last few years, that all track bed problems which would include ingress of water to the subway from the track, have been resolved. Nonetheless LBL should seek assurance from NR that this problem has been fixed and thereby that the project is not at risk from circumstances outside its scope and control and potentially find themselves in a position that water ingress is still an issue after completion of the works.
The attached cladding drawings are informative in that they clearly depict an early design stage and are not construction drawings especially when the designer has marked the drawing with a note that the client is to specify the height of the cladding - this might be a pointer that not all of the design risk has yet been fully addressed.
Ceiling cladding can be a major benefit in that it can be designed to channel moderate quantities of water to the sides of the subway for collection and draining away. The downside is that NR can be very specific in requiring a material and installation standard that is higher than the construction norm for non-railway work. This of course can be appropriate when you have high speed non-stopping trains thunder over the subway that can cause significant degrees of vibration and deflection thereby requiring correspondingly robust fixing systems. Equally NR's approval process for design and/or type-approval can be onerous in both time and money.
NR's definition of betterment also needs to be carefully addressed. The concept of betterment in NR terms often attempts to obviate the fact that assets need to be renewed from time to time and thereby despite evidence that may prove that an asset needs to be renewed, NR may argue that funding cannot be made available as the required renewal would be deemed to be "betterment". NR and TOC's frequently refer to the asset being in a condition called "steady state" that often ignores the industry's standards for definition of what a modern stations facilities should be.
This problem is a microcosm that is embedded in Thatchers privatisation of the railway which became a lawyer's paradise of legal speak and redefinition of common sense.
This scheme needs a robust approach to these issues if it is not to be further mired in delay and under-estimated costs.