SAN FRANCISCO/TOKYO—Apple will let some apps like Netflix provide links to their websites for user payments, a small concession that would allow app developers to bypass the controversial 30 percent App Store fee the iPhone maker charges. The concession was part of a settlement with Japan’s anti-trust regulator, which said the change was enough for it to close a five-year investigation into Apple that focused on video and music apps but did not consider games. The U.S. tech giant, however, must still contend with a raft of other legal and regulatory challenges, including a closely watched antitrust lawsuit brought by “Fortnite” creator Epic Games. The ban on providing separate links on App Store apps was lifted for so-called reader apps that provide content such as e-books, video, and music, that do not offer a free tier of service, and require payment at sign-up instead. Currently, apps like Netflix and Spotify …