With a little more digging, I think I've got the sequence better figured out.
First you had the first version of the GA-40 with 6SJ7 input tubes and a very different amp circuit from the following versions.
Second, you had the 5879 version with the input resistors configured to pad down the guitar signal before getting to the 5879 input tube. I guess they didn't want you to be able to overdrive the input pentode. This is the two-tone oatmeal/oxblood cabinet with the brown control panel.
Then, you have the third version with the inputs changed to a standard 1M input impedance with the full guitar signal going into the 5879, so even though the amp isn't that different, it interacts with the guitar differently, allowing you to push the 5879s a lot harder. This would be the two-tone tweed version and then the all-tweed version with silver control panels.
Does that sound right to Gibson experts?