My opinion (not worth much) is that when John Linebaugh did penetration tests with all the wimpy cartridges coming out on top, and also when Garret did his .45-70 tests, was that they were using semi wadcutter or LBT type bullets in their favorite loads while taking more powerful cartridges loaded with everything else. I think the results they got are far different than they would have been if all cartridges had been loaded with the same bullet type.
You can try a test yourself. Take a .44 magnum revolver loaded with Elmer Keith's old load of 22.0 grs 2400 (Hercules 2400 I think) and a 250 gr Keith type bullet and compare it to some randomly selected .30-06 factory ammo in terms of penetration. The lame .44 magnum load will frequently penetrate as far or farther, unless factory loads got a whole lot better since the last time I used a .30-06. I tried this myself when I was about 17 years old after reading it in an article written by Keith and got the same results he did. At the time no company loaded premium bullets for a .30-06 and if they did I couldn't have afforded it, so my testing at home was limited to factory .30-06 loads from Remington and Winchester vs my .44 mag reloads made according to Keith's recipe.