Win anything from the eShop roulette wheel

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) .

Even though they are "duplicate" Miis as far as you are concerned, they are 2 separate Miis as far as the system is concerned.

If you deleted the Mii that was imported from the 3DS, then any content tied to that Mii would be gone. Consequently if you deleted the Mii that was imported from the Wii, then any content tied to that Mii would be gone. Ergo, if you deleted the Mii that was imported from the Wii, then that would cause your Super Mario Galaxy 2 to revert as well as any Wii-specific data.

I tried this by "duplicating" a Mii using my 3DS, original Wii, and Wii U.