The immigrant visa fees, the medical examination, document retrieval, translations and any professional representation you engage all sit outside the gift. Only the US$15,000 processing fee is stated to be non-refundable; the treatment of the other charges depends on the body collecting them, so ask each one directly. For each amount, ask who receives it and who can refund it. A government body, an authorised physician, a translator, a registrar and any representative you appoint each set their own terms, and none administers another's money. Put the question to the collecting body directly rather than to whoever quoted you a total.
What the US$1 million gift is and is not, financially
The gift is not EB-5 capital. It buys no shares, creates no job requirement, and comes with no promise of dividends or repayment. Once transferred on instruction it functions as evidence of the specified benefit and eligibility, rather than a purchased interest in a business.
Treat the US$1,000,000, the US$15,000 fee and the ancillary charges as three separate lines when you plan. Budget the personal exposure the payment does not cover. The transfer discharges no other obligation, so travel, translation, document retrieval, the medical examination and any professional representation continue to fall on the applicant.
Permanent residence, once granted, carries consequences worth pricing in advance, including worldwide income tax reporting, and a decision of that size deserves advice from someone qualified in tax rather than an assumption drawn from immigration materials.