Ok, so I found out I have some UGCs that differ from the ones mediashelving.com is selling. They're a bit thicker than one inch and have a different inside structure. Here's a picture:

These boxes have the same problem with SNES/N64 manuals however:

BUT, since these boxes are a bit thicker, they are able to close properly with even a thick manual or a manual with a bunch of other paperwork. This is a picture where there's a US SNES cartridge underneath the manual, WITH a plastic dustcap on it as well:

So wouldn't you all agree that this thicker (probably older) UGCs are a lot more convenient? I mean what's the point of boxing your games when you still have to store the manuals somewhere else? And does anyone know who manufactured these and where I might be able to buy some?