Replacement for fileEntry.toURL() in Chrome Packaged Apps
Have you tried using chrome.fileSystem.chooseEntry? This API lets your app save files to the user's hard disk, wherever they want, letting your program have a Save As kind of command. This is a bit different to a download link, but is also more in harmony with V2 apps being like native apps.
chrome.fileSystem pops up a dialog asking the user to choose a location for a file. If you use the options for saving files, this returns you a file entry that has permissions to write to the location chosen by the user. The user can also create new files when you use these options.