If the chain store pharmacy gives a prescription discount to employees, I am not sure why you wouldn't want to take advantage of that benefit.
Of course you can get your prescriptions filled wherever you want to, but it can be smart to call and compare costs. Drug companies often "pair" with certain pharmacies and these pharmacies will offer lower cost.
For a Michigan example: At Meijer's pharmacies, you can get amoxicillin for free whereas it can be expensive at other pharmacies. At Walmart pharmacies, you get a better price on insulin.
The pharmacy is your choice but, because drugs can be costly, it pays to shop around.