旗舰 is flagship, but 旗舰店 is not a shop where a flagship is on sale, right? If it is a shop in relation to flagship, the meaning is not very clear. Because a headquarter is a better choice for that. So what is the real meaning of this phrase?
旗舰店 is just a direct translation of flagship store, which is used in english like this one: 5th Avenue.
Taken from the online Dictionary of International Trade:
"In retail business the designation of flagship is given to a retailer’s primary location, a store in a prominent location, a chain’s largest store, the store that holds or sells the highest volume of merchandise, a retailer’s most well-known location, a chain’s first retail outlet, a store location with decor or merchandise mix that is distinctly different from the rest of the chain, or the store location in a chain which carries the most high-priced merchandise catering to the most upscale customers."
Note that in English, a flagship store does not sell flagships either. And it differs from the headquarter in that a flagship store is a retail store whereas headquarter is usually offices where business decisions regarding the chain are made. Both in Chinese and in English, the word "flagship -旗舰" is used figuratively.