Is your ios mobile device using firefox or Chrome ? -> no only safari ... so your event putting your game in real fullscreen mode can't never work ... not working on a pc using chrome or firefox because of your "Is on mobile device" test .... and not working on ios because safari don't support this "Browser request fullscreen" feature.
Your screen/layout size is good for a Iphone 3 ... Ipad use bigger screen or perhaps you are speaking about Ipod touch and not Ipad ?, i will try to do some tests on iphone 4, sorry i have only that ;-p
Ok i think you are speaking about Ipod Touch ;-p ... the problem is that html5 games use safari ... on the only way to have some good display without too many "bars" is to put your game as a "homescreen" application and then launch your game directly touching the new game icon and not launching it using safari. Using this mode the adress bar is not display but the status bar will remain on the screen ! ... and there is no way to remove it... so you will never have a true 480 px height display but a smaller one and this is why you have some problems because if your game height is resize from 480 to a smaller size, the width is resize in the same way never filling the screen.