The ultimate reason to obey civil authority is that God is the source of that authority. To see that this is so, we need to appreciate several interlocking points.
Since human nature comes from God, and humans are social beings then human society must be God’s idea. The purpose of society is the “common good”: those things that can only be achieved by common effort, such as truth, culture, and virtue.
The upshot of this is that not only does human society come from God, but so also does its purpose and the authority needed for it to attain its purpose. According to Catholic social teaching, the citizens can choose the leader, but in any case the leader’s authority comes directly from God.
Authority includes the power to command, permit, prohibit, and punish; but is limited precisely because God is its author. Any command or permission that requires or allows something contrary to God’s law (including the moral law) or undermines the common good (the purpose God has given to society), couldn’t possibly have any divine authority attached to it.
Regulations that prohibit activity of citizens can also step outside the bounds of legitimate authority. Yet, no right is absolute, since a right is what is owed and that can depend on circumstance. Hence the free movement of citizens can be curtailed for the sake of common good or to ensure justice for other persons or groups.
Still, in making this kind of judgment call, we need to cut the civil authorities some slack. These are prudential judgments, which are never precise.
Sometimes we are dealing with imprudent but not overtly immoral regulations. In such cases, the citizen should obey for the sake of the common good of a peaceful, law-abiding, ordered society: a great good.
Still, civil society is not the only society: there is the supernatural society founded by Christ, namely the Catholic Church. Her leaders are supreme in supernatural matters, as the civil leaders are in temporal affairs. Moreover, since the temporal life of man is for the sake of his supernatural destiny, the civil authority must give way to the supernatural authority when there is a conflict.
Hence, it seems to me that were the Church authorities to judge that, for the sake of the salvation of souls, her “citizens” need access to the Sacraments in a way only possible by the physical attendance at Mass, then these citizens would be obliged to disregard the civil authority in this matter.