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You could 3D print an insert cupholder that is any depth you like, that would just slide into the existing hole. I know its a bit more advanced, but there are lots of 3D printing facilities around now, and it would only cost around 100 bucks, even less if you did some research and learned how to do a lot of the prepwork yourself. Then there is oldschool plastic moulding that could yield the same result. If I had the 6MT, this would definitely be something I would make for my car.
Something like this. Although a 3D print file would be a lot more refined, and you wouldn't use a solid block, but some sort of honeycomb structure inside. This is just an example.