I put town portals in my belt, problem solved; you're not going to need 16 potions. Heck you could even use one column for ID scrolls. You're right though - it's rare - but personally and maybe for some others I don't like to end a run early if I don't have to. The only time I'd end a run early is if I die and retrieving my corpse just isn't going to happen (covered in a ridiculous boss pack). Some might just leave regardless to save them time, but I like to continue on if I can.
I personally leave a 4x2 space for items when I do magic find runs as I feel I have enough magic find and good enough equipment to keep them speedy, but there are times when I need more so I just throw down a town portal and ID stuff if necessary (I also tend to pick up a lot of stuff). If it's at the end of a run then yeah, save and quit with the item on your cursor is the way to go. I also leave my cube in my stash, but I can see the benefits of keeping it in your inventory. *shrug*