With games like The Wind Waker HD, New Super Luigi U and others, you have at least 3 savefiles. But if you download a new game digitally (through the Wii U eShop) and also buy the physical copy of the game, does it create a separate "channel" for the other version of the game? Thus allowing you to have twice as many save files?
No, you won't. The disc slot acts as a "variable" piece of software. If you check your save data in the Settings, everything to do with a specific piece of software (such as the Wind Waker HD, which I have both digital and physical copy), will be placed in the Wind Waker HD "folder," including the save-data for each user Mii and the software itself. If you want to have 2+ separate files, just create another user Mii on your Wii U. However some games, such as Game & Wario, are "universal" and all the save-data is shared throughout the Wii U. In order to get an entirely different save file for that, you basically have to get another Wii U (but Game & Wario has 12 in-game save files shared by everyone, just as the Wind Waker has 3 in-game save files shared by only that user) .