It literally means exactly that, take it up with the oxford/cambridge dictionary if you don't agree:
flagship
noun [ C ]
UK
/ˈflæɡ.ʃɪp/ US
/ˈflæɡ.ʃɪp/
flagship noun [C] (BEST PRODUCT)
best or most important product, idea, building, etc. that an organization owns or produces:
This machine is the flagship in our new range of computers.
The company's flagship store is in New York.
Jesus, you internet dorks will argue about anything lol.
Says the guy who just used a quote from a dictionary that shows that Flagship doesn't just mean best, it also means most important.
In case you don't get, you just proved the argument for the guy you were arguing against.