If you think that, you haven't read either the Court's decision or the Religious Freedom Restoration Act. This particular company didn't want to cover certain forms of birth control which it considered arbortifacients, but neither the decision nor the Act is limited to that fact pattern.
your reading too much into it. It is that a private company can refuse to pay for abortions of their employees if it goes against their beliefs.
what the supreme court really needed to do was back when Roberts(obviously blackmailed somehow) decided forced medical care could be considered a tax.