The Supreme Court has recently seen an increase in the number of religious exercise cases in which the conflict was caused by an act of administrative power, rather than an act of legislative power. There are probably several reasons for this increase, including the growth, size, and flexibility of the administrative state, political convenience, and the fact that administrators tend to be specialists who may be unaware of or undervalue competing interests like religious liberty.
While the sheer size, reach, flexibility, and specialization of the administrative state means we will likely continue to see more religious exercise conflicts caused by administrative power--and while there remains a danger of excessive judicial deference to agencies in these cases--in the long run this development can be positive for religious liberty. That is because the same attributes that make the administrative state likely to come into more conflicts with religious exercise (namely size, reach, flexibility, and specialization) also virtually guarantee that administrators will almost always have additional, less burdensome ways of achieving policy goals without burdening religious exercise.
The net result will be more religious exercise cases and, at least in the short run, more courtroom losses for the administrative state. In the longer run, either agencies will learn from these losses and use their size and flexibility to pursue win-win solutions in which they achieve their policy goals while working around religious differences, or they will continue to lose cases and build up a stronger body of Free Exercise and RFRA precedents. There are recent indications that both the Department of Justice and individual agencies are learning this lesson, which suggests that both religious groups and agencies will be better off going forward.
Mark L. Rienzi, Administrative Power and Religious Liberty at the Supreme Court, 69 CASE W. RES. L. REV. 355 (2018).