Have you ever seen the message Chrome, for example, shows for a quota request? Something along the lines of "this website is attempting to store more than x MB of data". To the uninitiated it *is* scary. The website is "attempting" to do something to your computer. Showing another message box before this one isn't going to solve anything:
"Now then, gentle user, your browser's going to ask you to do something strange, but you must say yes. Trust me."
That'll work. Typical developer reaction to solving showing one message box by showing two.
What we did is use the temporary storage, which doesn't require any permissions, and so doesn't show a message (or two). In testing the temporary IndexedDB (and FileSystem API) appears to have been permanent enough, with any data to be stored permanently done so on the server. So no messages popping up and happy users.
Carl