Did you bother to read the article? Right at the start it says these 200 workers "were each being paid about $1,000 every day".
Procurement practice and staffing practice are huge contributors to the excessive cost. The projects are massively overstaffed contrasted with comparable projects elsewhere - the article:
> "The staffing of tunnel-boring machines came up repeatedly in interviews with contractors. The so-called T.B.M.s are massive contraptions, weighing over 1,000 tons and stretching up to 500 feet from cutting wheel to thrust system, but they largely run automatically. Other cities typically man the machine with fewer than 10 people."
> "It is not just tunneling machines that are overstaffed, though. A dozen New York unions work on tunnel creation, station erection and system setup. Each negotiates with the construction companies over labor conditions, without the M.T.A.’s involvement. And each has secured rules that contractors say require more workers than necessary."
> "In New York, “underground construction employs approximately four times the number of personnel as in similar jobs in Asia, Australia, or Europe,” according to an internal report by Arup, a consulting firm that worked on the Second Avenue subway and many similar projects around the world."
The fictional no-show jobs that are pure corruption make up only a small amount of the cost of projects - a much larger portion are jobs are real, but largely unnecessary.
The other big practice cited in the article is that the unions do not negotiate with the MTA, but rather with contractors. Contractors, receiving a percentage of the total cost of the contract, have no incentive to reign in labor costs and staffing - and in fact have every incentive to do exactly the opposite.
A cheaper, smaller contract employing fewer people is worth less to the contractor. Realistically the city or the MTA should be negotiating with labor unions directly.