As a followup, I found that the
VideoRedo tool has a function to reduce the GOP length on writing.
For PS and Elemental output, this can be accessed in the Options on the Save dialogue box.
I found that for Showtime HD data, the GOP of 29 frames could be fixed by setting a maximum of 17 frames. This resulted in one extra I frame being added per GOP. So it takes some time to recode that frame for every GOP - but I think it is worth it since it is not a complete transcoding.