Not necessarily. The financial terms of a corporate sponsorship can bear on eligibility, because the source and authority behind the qualifying gift are part of what is assessed. Treating the clause as a private HR arrangement risks leaving it unexamined. Have it reviewed against the official instructions before you accept the offer.
Why the repayment terms belong in the immigration file, not only in HR
Two questions matter: who actually has authority to make the gift on the company's behalf, and what the company understands itself to be doing when it recovers the money from you. Corporate evidence about that arrangement may be relevant to the assessment of eligibility. A clause drafted only for payroll purposes can describe the transaction in language that does not match the program's, which is a reason to have both documents read together. Also obtain advice on whether the proposed payroll deductions and repayment obligations are lawful and enforceable under the employment law that applies.
Admissibility to the United States, eligibility under the employment-based classification the program relies on, successful government vetting, and visa availability. The official FAQ retains eligibility for permanent residence, admissibility, and EB-1 or EB-2 visa availability as separate conditions.