The program amount does not change: the corporate gift is US$2 million, plus US$15,000 per person, and a spouse and one child bring the total to US$4,045,000. What the wage deduction changes is who ultimately bears the money, under your contract. The government gift is not a loan repayable by the program; any separate employer–employee debt must be assessed on its actual terms.
Separating the program amounts from your net position
Work out the after-tax effect of a deduction with an accountant, on your own numbers, rather than assuming a rule. Note too that only the US$15,000 per person is described as non-refundable — that is not a general refund entitlement for anything else, and not a statement that everything else is lost. Government, medical and professional charges sit outside these figures, and a written professional quote can cover them.
Corporate terms describe 1% annual maintenance and a 5% transfer charge including a new background check. The required gift is paid by the applicant to the U.S. government following successful vetting and instructions; it is not an equity purchase, a repayable investment or EB-5 capital.
Under the Gold Card the money is a gift to the U.S. government: it is not invested, it creates no jobs by definition, and it is not returned in any circumstance.