Because she wears both outfits. The Captain outfit is the one she wears while on land and on formal occasions, the default one (or the LoR variation) is the one she uses while at sea.

According to Riot's lore team, MF finds the Captain outfit too stiff to move in and overdressed. It's actually realistic. She's not the type of captain to bark orders from the quarter deck while everbody else do the hard job. She'll be constantly going around and zipping up and down jacob's ladders. A heavy coat is only going to slow you down.

Also Miss Fortune is one of the female "cake characters" of the game, along say, Ahri, Katarina Morgana. While Riot has diversified the fanservice, even introducing guys, MF, Ahri, Kata, Morg still are the original "hot busty feisty ladies" and Riot doesn't want to change that.