Agreed. It's definitely a hassle, and I hate it as well. (What might be worse is putting a hidden track in "track 0", since iTunes won't rip it and you won't even know it's there unless you hear about it. cdparanoia will rip it, though.)

The hassle-full fix is to use iTunes start/stop times to select the first song, "convert to AAC", change them to select the second song, repeat, and rename the files appropriately. PAIN IN THE BUTT.