A Supreme Court case about one type of payment to Obamacare insurers could provide answers to an onslaught of lawsuits against the federal government over billions more the companies say they’re owed separately.

Two different provisions in the Affordable Care Act contain language to reimburse insurance companies for covering people with costly illnesses or low incomes. Both are being litigated because Congress has declined to provide adequate funds to pay the insurers, which means the companies are getting far less than they were told, or nothing at all, to cover high-risk people.

If the justices agree the government committed in...