Two different mandates, but your point might hold. The one that was just challenged that SCOTUS ruled on was the mandate that individuals must buy insurance. The HHS mandate against churches is a regulatory rule stating that all health insurances must include abortions.
The problem occurs if you have a penalty (tax?) for not offering insurance. But also if churches desire to offer insurance.
So it is really two issues. Can congress apply a penalty (tax) to a church for failure to offer insurance. And can Congress limit insurance offerings in such a way that there is no insurance alternative available to churches that don't violate their conscience.
I see your point. But wasn’t the HHS mandate issued as part of Obamacare?