Welcome to the magic of cost-plus.
Unless the cost consultants / quantity surveyors got their qualifications off the back of a packet of cornflakes cost-plus would be established from a fixed baseline not percentage linked to the overall scheme value.
There would be cost being the actual quantifiable amount spent by the contractor/consultant and the "plus" being a pre-agreed margin to cover overhead and profit.
A design/engineering consultant should thus submit timesheets listing out the time spent by each resource level e.g. junior engineer, senior engineer, daughtsperson, document controller, design manager etc... The contract would list an agreed rate for each.
A contractor would do the same listing out, plant, materials and resources all using pre-agreed rates.
The client then has to manage this to stay within budget (or not).
What contract have NR selected for contractors and consultants on GWML?
Crossrail as an example went for NEC3 with consultants on framework agreements and contractors on Option C Target Contract (aka risk sharing between client and contractor).
One would hope NR have not selected a management or cost reimbursable contract. As doing so requires very strong project and cost management to stay within the projected figures. The other forms are more likely to aid in cost management if only because the contractors/consultants will scream for variations for anything outside of original scope which should make it simpler for the QS's to realise the budget is done for.