As far as I know, there is absolutely no mention of the different versions in the dev docs.
I did some limited testing a while ago. If I remember correctly, one of the two ROM versions seemed to work regardless of the hardware version ; the other one didn't work reliably on one of the two hardware versions (it didn't boot every time).
I didn't look into it in depth, but one of the differences between the ROM versions are the values used to initialize the video registers: some of them are different.
It's an Atari console. What did you expect?