townies examples (at least the first two) are not about freedom. We aren't a theocracy and I am grateful for that. Everyone in this country is free to use birth control. Catholic universities are not free to run their universities in accordance with their faith if they are forced to cover birth control as part of their employer provided insurance.
But they are taking government funds. In any business, if you are a primary source of capital to a business, you often set rules. this is no different.
My first two examples were also about freedom. If the mandate holds up I am no longer free to make decisions about my health. I am also not free in the state of North Carolina to smoke in certain places.
Your examples are not about freedom as they directly other people. You have no right to cause others to pay for your actions. Whether you are in NC or anywhere else, you have no right to cause me to have my clothes cleaned so you can smoke. You also have no right to impact my health via your smoking around me.