"I missed the part in the Bible that set zoning and occupancy requirements for Christian churches"
Try Romans 13:1-7 and Titus 3:1. We are all under authority and government was established for the common good. If we don't like the laws and civil ordinances we can address them at the ballot box. Zoning, occupancy, parking, building, fire and health codes do not hinder the spread of the Gospel, just the size, location and kind of structure.
I believe when the govt told Daniel not to pray HE DISOBEYED We also have something called the separation of C & S
I should have clarified. That was directed at folks who critize big churches for their architectural design and number of parishoners (as though design and occupancy levels were scriptural), not at government regulations, though I can see I didn't make that clear.