Either Thom Hogan is totally clueless, or it's again related to D300 read noise due slower data from sensor. Once you leave the base ISO, the extra bits should just be noise and nothing else.How many times do you use higher ISOs? That's where Thom Hogan says he sees the biggest difference between 12 bits and 14 bits on the D300, and it makes perfect sense.
And this time I will take your D3 challenge. Do you have examples from D3 at ISO 400 and up that show a difference between 14-bit vs 12-bit?