I think your decision depends on your outlook.
Under the description in the Union Twp ordinance you described (coop 200 feet from a property line), you would be in violation anywhere on your property.
That being said, you are going to have to ask yourself: "Do you own your property or does Union Township actually "own" it?"
You are going to have to decide whether you have property rights or not and whether you are going to stand on your principles or not.
In my situation, the city encroached on us five years ago (no vote for those of us affected). They have an ordinance against keeping roosters. I have several anyway and have ejected their code enforcement people from my property on multiple occasions under threat of having them arrested by the county sheriff for trespassing. It took them about three times to figure out that I was dead serious. The end result was that their supervisor ordered them to never step foot on the property again. (That was after I informed him that if his agency continued to try to exert such nonsense, I would not only sue them, but also him. They got the message and found an easier "mark" to try to revenue from).
This much I can say, much of it will probably depend upon your relationship with your neighbors. Bad neighbors can give you many headaches, while good neighbors will protect you.
If you are on good terms with your neighbors, it can't hurt to go to them and explain your intentions and concerns.
Offers a few fresh eggs sometimes help!