Nevertheless, there is a fairly high chance that the Supreme Court will rule that broad exemptions for religious objectors are mandatory, regardless of whether the incumbent administration supports those exemptions. It is less clear, however, whether the exemption for “moral” objections will be upheld.

What’s happened in the legal fight over religion and birth control so far

Until about six years ago, religious objectors stood on very weak ground if they sought to deny a right to their employees. As the Supreme Court held in United States v. Lee (1982), “when followers of a particular sect enter into commercial activity as a matter of choice, the limits they accept on their own conduct as a matter of conscience and faith are not to be superimposed on the statutory schemes which are binding on others in that activity.”

Thus, an employer generally could not impose its religious views on third parties that do not share those views.

The turning point came in Burwell v. Hobby Lobby (2014), after regulations promulgated under the Affordable Care Act began requiring insurance plans to cover contraception. Hobby Lobby held that the federal Religious Freedom Restoration Act (RFRA) allows many employers that object to birth control on religious grounds to exclude contraceptive coverage from their employees’ health plans.

Hobby Lobby was hugely significant as a matter of legal doctrine, as it effectively eradicated the old rule that religious objectors many not undercut the rights of third parties. But the Court’s opinion in that case appeared to be fairly limited in scope. Justice Samuel Alito’s opinion for the Court leaned hard into the fact that, rather than requiring all employers to provide birth control coverage directly to employees, the Obama administration could have achieved the same goal more indirectly.

Under this indirect approach, an employer could “self-certify that it opposes providing coverage for particular contraceptive services.” Once that happened, the government could make a separate arrangement with the insurer that runs the employer’s health plan, which would ensure that the employer’s workers receive coverage for birth control.

After the Obama administration took up the Supreme Court on its suggestion that it use this more indirect method of providing contraceptive care, some religious employers objected to the process the Supreme Court appeared to endorse in Hobby Lobby. The result was a second round of litigation, which culminated in the Zubik decision.

Yet with the Court apparently split 4-4 on the proper outcome in Zubik, that decision did little more than punt the case back to the lower courts. The broader question of whether employers can wield their religious objections to deny birth control coverage to their employees remains unresolved.

The two sides in the Pennsylvania cases want the Supreme Court to decide vastly different questions

The striking thing about the briefs in the Pennsylvania cases is that the two sides want the justices to resolve very different issues. The states challenging the Trump administration’s regulations push for a narrow, highly technical decision tossing out those regulations because the administration did not jump through some required procedural hoops.

Meanwhile, both the Trump administration and an order of nuns that hope to preserve the administration’s broad exemption for religious objectors ask the Court for the same sweeping victory that religious conservatives sought in Zubik. (The order of nuns, known as the Little Sisters of the Poor, are not an original party to this lawsuit, but a federal appeals court permitted them to “intervene” in the case, thus giving them many of the same rights to litigate the case as an actual party.)

As a general rule, federal agencies must go through a process known as “notice and comment” before a new regulation can take effect. Under this process, the text of a proposed regulation is made public so that anyone can comment on it, and the administration normally must respond to these comments before the new rule can take effect.

But the Trump administration bypassed notice and comment when it created the strong exemptions for religious and moral objectors at the heart of the Pennsylvania case, although it did retroactively put the exemptions through notice and comment after they were already in effect.

According to a federal appeals court that struck down the exemptions, this backward process is not allowed. Though the administration argued that it could bypass notice and comment because of “the urgent need to alleviate harm to those with religious objections to the current regulations,” the lower court rejected this argument.

“All regulations are directed toward reducing harm in some manner,” Judge Patty Shwartz explained for the lower court. So if harm reduction were sufficient reason to bypass notice and comment, that process wouldn’t need to exist.

If the states convince the Supreme Court to embrace a similar rationale, that will delay resolution of the larger issues presented in the Pennsylvania cases, but it probably won’t do so for long. The Trump administration could always reinstate broad exemptions by going through a proper notice and comment period. And even if Trump leaves office before this process is complete, religious objectors could still file a new lawsuit claiming they have a statutory or constitutional right to deny contraceptive coverage to their employees.

Meanwhile, both the Trump administration and the nuns argue that the broad exemptions supported by the administration are mandated by law. As the nuns claim in their brief, the RFRA “not only permits, but affirmatively requires, the Final Rule.”

Indeed, the Trump administration argues that the very same self-certification process that the Court appeared to endorse in Hobby Lobby does not provide enough protection to religious objectors. “As became clear in litigation following Hobby Lobby,” the administration claims, “some employers hold the sincere religious belief that participating in a process by which their employees receive contraceptive coverage ‘makes them complicit in providing [that] coverage,’ even if the coverage is actually paid for by other parties.”

And so, the administration claims, these religious employers have an absolute right to refuse to participate in any way in a regime that helps provide contraceptive coverage to others, even if it means than many individuals will be denied access to birth control coverage. . .

(Excerpt from Vox. Article by Ian Millhiser.com)