interesting theory it could be true, in a way naruto's chakra does seem stronger. Although aside from the mixing Naruto's chakra could be stronger just because it is constantly fighting off the kyuubis making a never ending stamina battle. In either case naruto's chakra becomes stronger and more plentiful. hard to say nice theory though.
In the fight with Orichimaru When naruto was in 4 tails mode. The Super Condensed Chakra was made out of Red Kyuubi and blue Naruto Chakra. at least in that situation it was not mixed. But the kyuubi did infact mix it together to make the blast.