Ugh, I have the same issue. The one game that I have on iTunes is 4:3 for the iPad, but the build indicated for all devices, so I had to upload all the jpgs. I wasn't able to find anyway to get around this, except to indicate this in the apps information to the customer. With that said, there was a tutorial on this site to make your app fit on most screens, the steps are below (this is for games that don't have scrolling parallax):
1) Under "layout properties", set the layout size to the iPad size: 1024, 768 (ratio 4:3 - same for ipad4), AND set "Unbounded scrolling" to "yes" - do this for all layouts in game. Note: when making the artwork, make double the size so on larger screens it won't look bad.
2) In "properties" under "Configuration Settings" set "Fullscreen scaling" to "Scale outer", also set to Landscape or portrait
3) In Project settings, set your window to 1024, 768
Make sure all sprites and anything else are far outside the boundaries, or they may be seen.