This isn’t a surprise: comments are meant to ensure that rule-making agencies consider relevant information before making a final decision; they aren’t an opinion poll. See the Administrative Procedure Act, 5 U.S.C. § 553(c): After notice required by this section, the agency shall give interested persons an opportunity to participate in the rule making through submission of written data, views, or arguments with or w…
Are you suggesting that only legal arguments or facts are relevant? So an actual analysis (which would necessarily include predictions that are not certain) of the impact of a decision is irrelevant?
Political appointees are entirely within their power to ignore such comments.